I found this to be the biggest issue with using Colemak or any other alternative layout. I use my own computers exclusively so I had complete control over using my layout, but it just got so tedious having to rebind everything all the time and I would often run into games and programs where you couldn't rebind keys at all. Trying to rebind keys to work in a sane way in Emacs was an uphill battle that never ended.
Why not just buy a keyboard with a layout switch button. No program will force you to use qwerty if your keyboard manages layouts. But seems like no such a keyboard is out there. Couldnt find it on Google or Amazon.
The TypeMatrix has such a button (Dvorak Key). It remaps the keys at the hardware level. It's accessed with Fn+F1 and has a LED indicator on the left side.
I found this to be the biggest issue with using Colemak or any other alternative layout. I use my own computers exclusively so I had complete control over using my layout, but it just got so tedious having to rebind everything all the time and I would often run into games and programs where you couldn't rebind keys at all. Trying to rebind keys to work in a sane way in Emacs was an uphill battle that never ended.