That is only the case if you think you have to press Ctrl using your pinky. You can use the side if your palm instead. Then CUA suddenly becomes very ergonomic. Try it. I've done this for over 15 years now across a plethora of different keyboards and also survived several years of Emacs unharmed thanks to it.
I used to do approximately this, from maybe the mid-90s to 2015-ish, but finally that keyboard died (RIP dear friend) and I find that it doesn't work properly on any keyboard I've found since.
Not quite the side of my palm, but the joint where my pinky meets my palm. My hands are relatively large, dunno if that's relevant.
I should put more work into buying a keyboard that it does work on, I think using my finger for Ctrl might be starting to cause RSIs in my middle-aged hands.
I guess I'll also add that for me it's a bigger deal when gaming than when using CUA. That Ctrl button is the one true place to put crouch, dangit.
Most of the time the joint that you describe works for me. Sometimes I use the side of my palm. It has worked for me on pretty much any keyboard so far, regardless of the height of the caps or the travel. On those with an fn-key I have had to remap the key somehow, sometimes in the BIOS sometimes using software. The exception is a smallish bluetooth keyboard I bought for a tablet. It's fn-key is hard to remap inside mobile OSes.
How do you do that without hitting Shift? It seems needlessly finicky compared to just properly holding the key down with my pinky. I'd say the best way to avoid RSI while using key combinations is to follow proper procedure and hit the opposite modifier, e.g. Left Control + S (Right Control for Qwerty typists).
It's probably due to my shoddy description. You put your fingers into the touch typing homerow. Shift your left hand enough for the edge of your palm to be above the ctrl key. It might also be the base joint of your pinky, depending on the size of your hand. Now press that side down enough to activate the ctrl key while keeping your fingers on the homerow. It's like having an eleventh finger to control the keyboard.
It doesn't make sense to change Vi/Vim/NeoVim keybindings because they're so convenient, composable and easy to remember.