Shortcuts don't work right if you use Colemak

I have a non-standard keyboard layout Colemak which I made to work so that all shortcuts are like when using QWERTY. But they don't work that way in Speedcrunch. For example, in place of letter S, I have letter R, but when I press Ctrl+R, it registers like usual Ctrl+S in nearly all programs, except it doesn't work like that here.

OS: Windows 10, 1909