Good news everyone!
After much kerfuffle and an excess of faffing about, I believe that I've fixed the resolution scaling issue. I've only got a 2560x1080 monitor to test it out on, so I can't be 100% sure it's fixed, but I've tried out every resolution I can and it looks like the fix correctly scales and positions the game window, while also killing the mouse offset problem that was happening alongside it.
Fixed(?): Resolution scaling issues.
Fixed(?): Mouse coordinates were being incorrectly offset from the visual position.
If you are still getting issues around game window scaling, positioning or mouse offsetting, please let me know, with a description of your current resolution and how the game window is behaving! I appreciate the bug reports!