No conflict as the CPS has nothing to do with the tranny. Now if you did do what you are thinking/talking about, it would be an interesting test to see if you used a lightweight flywheel in your car to see if you got a CEL or not. The 2 CPS/STi/No CEL vs 1CPS/WRX/CEL with a lightweight flywheel is just a theory.
There is no safe weight as car A responds well to flywheel A and car B throws a CEL with the exact same flywheel.
The CEL is NOT vital. All it is, is an annoyance. You can drive normally with that "missfire" CEL and be fine. It isn't one that puts your car into limp mode or anything.