I think this is an important concern, but not a disqualifying one. There is already a lot of variety in the space of controls, for example compare browser controls to the Office Suite to native OS, it's a big spectrum. When controls are customized correctly they become more usable within the context of the app because they are sized consistently, line up with the content grid, follow visual cues from the rest of the app, etc.

Maybe you can introduce smaller changes over a longer period of time? I dunno. Would not Windows users be stuck with that very old look if there were no changes? I mean, is this actually what you are favoring? That said, I cannot stand the trend of UI/UX on desktop being so touch-friendly, along with more padding and/or increased font sizes and less content, too.