> Emacs on Windows is especially awkward for me as a result of the QWERTY-on-Control behavior, because e.g. C-x C-t and C-x t now involve different positions for the T.

Okay, now that sounds absolutely maddening, mixing layouts in a single sequence like that.

The way of working you describe makes sense to me. I think you might be on to something with the bare letter keys used in Emacs combinations priming users to think one way and the positional, WASD-like nature of vi bindings pointing users another way (when it comes to basic cursor navigation). I use Emacs as well, with a mix of Evil and traditional bindings...

For now I'm glad that I'm just using one keyboard layout! Hehehe.