From what I have seen they will not let you apply from one country and receive elsewhere, though I can ask- it may also be that you cannot have an ETD running at the same time as a passport application.

In the Embassy it will be a change for them seeing as it obviously isn't somebody with an Isan bargirl in tow for once, so they'll be relieved about that and they will want to help you. I've never been there but I think you'd better get there early. Be prepared for a long day.
The #13 reply said, before you deleted it, that you couldn't get a Indonesian visa with an 'emergency passport' that isn't a passport.
Actually it said you couldn't get a VOA with an emergency passport - which you can't, it has to be a proper visa.
If you look at the link OP gave, emergency travel document is the same as an emergency passport - it's just terminology. That should be clear now.
You can apply for an emergency travel document (sometimes called an ‘emergency passport’) if you’re abroad, need to travel and can’t get a passport in time.

The British government, and that's who you're dealing with when you walk into one of their Embassies or Consulates, aren't going to want people to think that emergency travel documents and passports are one and the same.

They had closed by 1 this afternoon when I tried calling. We're in Chiang Mai and I obviously can't fly... May be able to get partner to go in my place but after calling if it is an ETD I am getting then will have to hold back til we can get everything else in place as the dates of entry need to be in the ETD.
I was so sad to see my limp passport, I won't feel right til I have a fresh one lined up with the others in my pouch.
LOL since the web-site IS the official British government foreign office web-site, I don't think they will be confused.

The big difference between UK passports and emergency travel documents is that UK passports have a chip while the emergency travel document does not, plus there is the five country limit. If you are going to a country that requires passports with chips or you have to get a visa (e.g. the US) then you are out of luck, there is no problem if you get the emergency travel document within the US but if you are in Central America where almost all the flights back to the UK require transit through the US then it is a very big problem but in South East Asia it is less likely to be a problem.

It has to be Bangkok. You have no chance of getting the Indonesian visa you say you want in any other place.
You don't need a passport, to get on an internal Thai flight. Any photo ID, like a drivers license will do.
Besides what's stopping you from taking the train?
The idea of having your partner doing it on your behalf, is the biggest laugh ever. Of course they can't.
You've got to get your ass outside the British Embassy in Bangkok on Monday morning. The Embassy, for once, isn't going to want to know about your partner.

I know it is only Bangkok. If it was to apply for a passport it specifically says someone else can apply on your behalf, probably not for ETD as should be produced on same day. I have a small child I would have to bring with me. I don't have a driver's license. However, I have no intention of going to Embassy prior to calling as an ETD (if that is what I need to get) does not require weeks to make and I would need dates of entry put into it which I do not have. I do not see why, if they will not post to a different country to application, that I do not travel through Bangkok once ready to go that way, pending conversation with embassy.
My question was only about entering Malaysia with an emergency travel document and you have been persistent in telling me how much harder things should be than the official advice online (and anecdotal, forum stories) I have read. I already travel with a disabled child (hence the things placed up high), I have more than fair share of struggles.

somebody else can apply for a passport on your behalf, but when you are not there, somebody else who is like an honorary member of society, not part of your family, and WHO HAS KNOWN YOU FOR A LONG TIME, has to countersign the photos to say that they photos are a likeness of you. You are not likely to find somebody like that when you are on holiday, unless your family doctor on holiday happens by a fluke to check into the same Chiang Mai hotel that you are staying in.
you have to go down to Bangkok and get to the Embassy right away. Forget about calling them or emailing them. Forget about going online for 'information' that may or may not be accurate. You won't be the first person that's turned up there in this kind of situation and they'll be able to tell you if you can enter Malaysia, leave Malaysia, enter Indonesia, then leave Indonesia, and then return to Bangkok to pick up your replacement passport when it finally arrives. The longer you delay getting down there to Bangkok, the longer you are delaying getting your replacement passport. You want to be getting the train down there tonight and be lining up outside there tomorrow morning.