When auto accept is enabled, and a file transfer comes in, the conversation window automatically gains focus. Is there any way to avoid this? Or maybe change it in a future release?

Note: other events may grab focus as well, I haven't tested them.

From what I know, no.

I think it works be brining the window into focus and pressing Alt+C (or whatever the shortcut is) so at the moment, there's no way to stop that since the window needs focus for the shortcut to work, sorry.