Borneo the jungle has much fewer animals. Congo has the large animals (elephants, gorillas) although numbers are dropping and the Amazon has many animals but not large ones.
It's straightforward to get to 'lodges' but tough to go in deep and it's difficult to find 'trusted' companies that can actually take you on first time expeditions or on really off-the-beaten-path treks.

Sarajevo is one of the most magical cities in Europe even, imo. Also it is said that the train ride between Mostar and Sarajevo has stunning views (cannot tell you first hand since we drove, but even driving there we drove through the most beautiful scenery).

Sarajevo and also most of the rest of the Balkans, will already feel quite off the beaten path except from some very touristical places like Dubrovnik and Plitvice (which are definitely worth your time!). So you do not really need recommendations that are not in the typical guides, imo. I could recommend you some in Bosnia, but still they would be in the Bradt guide, which is excellent btw. They would be harder to reach by public transport.

one more thing off topic.

if you plan on renting a scooter- get a international drivers licence before you leave. you can rent one no prob with out. its just they are cracking down- esp places like chiang mai. its a 500 baht fine. plus I never looked into travellers insurance policy-if you get really messed up ya might not be fully covered? just good to have one. less headache

I should have added - I will be flying into Barcelona and out of Madrid. We were able to get super cheap tickets that way.

I also enjoy gothic architecture, authentic food, and walking around narrow streets.

I've done high paced Europe tours in the past and this is the first time I'm not doing one. On those tours, we spent 1-2 days in each city and I found that to be just enough. Which is why I was ok adding another 2 days to get a glimpse of another city.

I also have checked and there is an overnight bus between Lisbon and Seville. It leaves Lisbon at around 9 I believe and arrives around 730ish (times might be a little off). We would then do the fast train from Seville to Madrid which is only 3 hours.

Something else I'll add, is that I go off cycling during my spare time and have found many true gems well off the beaten track, but I guess that isn't really an option if you live in Beijing. I'm lucky in that I can be out of the city in 20 minutes and then just set off wherever the fancy takes me. Even in tourist hotspots like Wulingyuan I borrowed a bike from the hostel and set off on my own away from the crowds. Consider hiring a bike and touring around this way.

In Mauritania...
One dad, two boys and a bag...
The journey to the oasis..
We got up early to avoid traveling some of the heat of the day. Got a ride through Nouakchott passing donkeys and carts loaded with barrels of diesel , and camels galore and all the other early morning activities of a sleepy desert city before the rich have risen to dominate the roads with there faster moving fury. We got dropped at le garage, where mini busses leave from, bought bananas and oranges from a roadside vendor, chucked our bag on the roof and climbed on the “bus”. Then out into the desert, the massively varying desert. The sand and rock going from red to bleached to black to combinations, from barren and battered , scrubby to drifting dunes to harsh and craggy black rock mountains. The monotonous chanting of prayer blares constantly from a speaker next to us the entire journey. Nomads randomly camped, seemingly miles from any apparent reason to be there , their homes varying visibly in construction from what is available, from tents to grass huts to intricately woven domes of date palm leaves.. to sticks and patchwork quilts of rags
The colours of their costumes like that of Rajasthan and other Gypsies of the world.. the sand and dust and heat intense, making it impossible to open the window, for the sandstorm rips at your face and eyes.
After some hours we stop to drop someone off, alone in the desert like a man on the moon! Sometime later a passing pickup flashes us down, as the roof net has come loose and some luggage had fallen off... we retrace our steps and find someone’s new door and frame they’ve been to buy from the capital has blown off and is lying in the sand, no one bats an eyelid, just a vague murmur through the bus, it’s reloaded and off we race.
We stop again in a village where vendors sell sandwiches of desert bread, cooked in the sand beneath fires and camel or goat meat grilled on charcoal there and then. And drinks. People are all so caring of the children, although confused by the absence of a mother or wife..
After five hours since we left Nouakchott, we stop again, at a shack by the roadside, the road is rising, the land rocky, we are about to ascend a pass, the old men get out, rapped in cloth and go to the hut, where they pass a wooden bowl presented them. One weathered man comes and blesses the minibus, muttering and throwing handfuls of water on each wheel. Then they bring the bowl and pass it round the bus for us all to drink from. An ancient looking bowl , in it is, I think, from what I understood , whey from camels milk, and sweetened slightly, we each take a drink and it is amazingly refreshing!
After six hours, we stop at a junction and a police check point, maybe the eighth, the boot opens, it’s our stop, and we clamber out over the backs of the seats. The gendarmes come to inspect our papers, more confusion over the missing mum, “it is very complicated to look after children for a man!” The police agree they will flag down a car to get us the last 12 km to the oasis. It is so hot! There’s a stone shack, a palm leaf leantoo and a date palm shack. They tell us to take shelter from the sun. There’s a few of them in the palm shack and they point us to the other, where we find a sleeping policeman, and some young goats and a puppy tied up together. After not too long a beaten old merc is flagged down and we climb in. We hurtle along through canyons and sand past a village of palm leaf homes, until we stop, as up ahead a car is stuck in the sand and blocking our way. we sit and wait and bake for 20 mins or so, before they move a bit, we then plunge at the sand, and incredibly glide through it. The driver stops alongside the other car, now stuck again and lets down their tyres for them so they can better drive on the sand... jurky arabesque music blaring, we bump and bounce our way to the oasis, or a few hundred meters short of it and stop in a date grove. We are led through the palms to a little encampment of nomads tents and a large roundhouse thatched in woven palm with a sand floor and rugs and cusions, where we are invited to rest. Moments later a grate stainless bowl of cuscus and veg and goats meet is presented us, water to wash and drink. After we have feasted, the boys find some kids (baby goats) to play with and I recline!
After we have rested, we set off for the oasis proper. We wander along the sandy track a while, before we bump into our host to be, jamel, who family or tribe apparently own the oasis. He takes Madog by the hand and they skip and dance of down the lane. There is a commotion and someone appears, trying to catch some goats, which Jamel lunges for and catches one by the leg. He points us in the right direction and we wander off and through the dust and rocks to the palms and much anticipated water! We meet another wizened man with fangs jutting from his face and two goats held around his neck and shoulders, his wife and daughter, who all exchange greetings and then we are there, the sound of trickling water, the coolness , little irrigation streams flow. The oasis is in a canyon, squeezed between cliffs, there are palms and between them are nomads tents with robed men lounging , the air full of chatter. Further on we find some women snoozing and cool on rugs beneath an outcrop of rock by a stream. A bit further we find a man face down in a pool and Madog and I start for a moment thinking him dead, but he suddenly moves and is obviously just luxuriating in the water. We start to clamber up the rocky steps following towards the source, and find some more women have rigged a screen , behind which we can hear chatte and they are obviously washing, so we scramble on and up and out the other side, more rocks and then dry dry desert!

Indonesia's central government, in charge of visa matters, doesn't really have the idea to encourage tourists to go off the beaten track. In fact they seem to expect us to stick to Bali, Yogya, etc.
The only area that at one time enjoyed special visa regulations were the Riau Islands, and then exactly because they were already very popular.
The only authorities interested in getting tourists to visit places off the tourist track are those of the regional governments, and they have no say on visa policies.

I used boats for river crossing both at Tiger Leaping Gorge and Xingping.
No problems whatsover at either.

I also visited Jordan using the free visa issued at Aqaba.

It sounds like renting a car might be the easiest route, and car rentals don't look too expensive - I got an international driver's permit and will plan to get a car for a day or two to explore the smaller villages around Strasbourg. If anyone has off the beaten path recommendations let me know - as I wrote above I'm hoping to visit La Volerie des Aigles in Kientzheim and Domaine Frédéric Geschickt in Ammerschwihr (if they are open to visitors).