git checkout mybranch
  git rebase main

Now git takes main and starts cloning (cherry-picking, as you said) commits from mybranch on top of it. From git's viewpoint it's working on top of main, so if a conflict occurs, main is "ours" and mybranch is "theirs". But from your viewpoint you're still on mybranch, and indeed are left on mybranch when the rebase is complete. (It's a different mybranch, of course; once the rebase is completed, git moves mybranch to point to the new (detached) HEAD.) Which makes "ours" and "theirs" exactly the opposite of what the user expects.