I’m trying to do that as well. I’ve been thinking that it would be nice to have some software that would disable specific chords when you use the “wrong-sided” modifier key for it, in order to train yourself to use the right one.
I couldn't figure out how to do this with QMK, I had the same thought as you.
Ok, more accurately I figured out that it would involve writing nontrivial amounts of C, and I gave up. You can do anything with QMK if you're determined.