key exchangeIt's Autocrypt, there's an RFC for it
So what about the reply-to email address? Or "on behalf of"?why would you need to set a reply-to header? I guess you could but why?
Do I mark large threads with the mailing list headers?it's not a mailing list and doesn't use mailing list style headers
Are group chats expected to support threads or always be flat?Flat for now but it's possible to change the subject of a reply to make something that would be a subthread. Some email clients kinda work that way. I've asked but this isn't planned because there's no real RFC for this kind of thing. If you want a "subthread" you can literally just use the client functionality to clone that chat to a new one, set a new subject for the subthread, and continue there. It's basically a shortcut for starting a whole new group chat is all, nothing special.