Hi,
Can't comment on the fees charged by the agencies but it makes sense that they would charge extra as there will be extra paperwork to produce on their part. Make sure you have all the papers you need to cross the border. There will also be some extra costs - for example you need to pay Customs for a cross border permit when entering Namibia (keep this as you will need it on leaving) and in Botswana you'll need to pay for third party insurance for the car. I can't recall the exact costs but if you look up the SA AA there is a spreadsheet listing exact requirements and costs at each border.
If you are on a budget I suggest you take camping gear. There are a limited number of places where you can get backpacker type accommodation and having a tent will give you a lot more flexibility. Bear in mind however that even camping at premium locations eg Sesriem (for Sossusvlei) and Etosha (if you camp in the park) are expensive ie c. $40 a night. Check out NWR for exact info.
Two things strike me about your intinerary.
Firstly you are spending time in some large cities (Windhoek/Francistown/Gaberone)which are a) difficult to drive and especially to park in with a limited amount for tourists to do. They certainly aren't where most people would head for when visiting the area but you may have your reasons.
Secondly there are big stretches of your itinerary you haven't allowed sufficient time for. The distances here are large and the roads often a lot slower than you'd expect (certainly a lot slower than SA).
So Etosha to Maun (jumping off point for the Okavango) via the Caprivi is at least two possibly three overnight stops. You will then need to arrange your trip and ideally allow a couple of days to do this. Many other parts of your trip will involve a full days driving to get there and you'll have to set off again the next morning so won't have time to do whatever you came for! Try and limit your stops and possibly your distance and have two nights in most places.
I suggest you get hold of the Tracks4Africa paper maps for both Namibia and Botswana. These will give you accurate journey times for the roads you want to travel. This is particularly important in Namibia where two roads that may look the same on an ordinary map but one can take 3 times as long as the other. Make sure you get a hire car with everything you need to change a tyre, blow outs are very common on the gravel roads and always carry extra water just in case you break down. The roads in Botswana are good tar unless you enter a game reserve in which case you need a good 4x4 (and they won't let you in otherwise).
Hope that points you in the right direction.
Edited by: itchyfeet38