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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.