Many newbs want this, but I see no point. After all, <Mod>+<letter> is <Mod>+<letter> for me no matter where the letter is. Keeping the shortcuts in their QWERTY positions eventually means having to remember the position instead of the letter. And I remember my shortcuts by their letters. In Vim especially, most shortcuts are mnemonic (and I use Extend arrows instead of the HJKL arrows) like b/e for 'beginning/end of word', i/a for 'insert/append' etc etc. I would not want to keep those by their QWERTY positions for sure!

On Windows you can achieve your "transmorphic" goals by keeping the VirtualKey codes from QWERTY while changing the layout output mappings to Colemak. This keeps the Ctrl+<letter> shortcuts as they were. But it comes at a price because you're cheating the system and I've heard that users have some issues with it.

Well, to each their own. I learned Colemak to enter vast amount of text comfortably. I'm not a fast typer (80 wpm, 100% touch typing).

When my fingers are in their default position on the home row, I'm in a "Colemak mode" and ready to type War & Pearce in a very relaxed and comfortable pace.

But, when sliding fingers to modifiers, or putting right hand on the mouse, my brain instantly switches to QWERTY mode. I can't remember where the keys are without placing my fingers back in the home row (it's 100% muscle memory), but it's not always comfortable to press shortcuts from the default position. Just the way I work.

Generally, I find shortcuts terrible to use with Colemak. E.g. some shortcuts designed for one hand can't be used comfortably. And, I'm 100% comfortable with this setup, if only I didn't need to switch layouts constantly.

I'm a tiny bit disappointed by the whole "you're doing it wrong, noob" vibe.

I'd also suggest considering sticky modifiers (ideally with timeout) - it's not very comfortable to do the awkward finger stretches using Ctrl/Alt etc on standard keyboards, whether using Qwerty or anything else.