Well, I've checked all documentation and looked at the source code.
Nope. Doesn't look possible as is, since this behavior is hard-coded into butler. :( Which is really, really, REALLLLLLLLLLLLY annoying, but isn't a dealbreaker. I thought there might be workarounds, like using butler to upload twice to the same repo but in different directories, which woudn't work. I can't think of a way. I suppose I can temporarily move game data to each build before uploading every time, which is less of a headache, but still frustrating.