In Pokemon, we don't use milliseconds for full game runs, but in Legends: Arceus we now have individual level categories that use an in-game timer that includes milliseconds. As far as I can tell, it's not possible to turn on milliseconds for IL runs only, but I just want to verify that I'm not just missing an option somewhere.
"Enforce MS" options doesn't work like that. All it does is ensure that submissions with 0 milliseconds will show "xx:xx.000" in the time column. (Instead of just xx:xx.)
The current way to handle it is to enable milliseconds in the game settings (which will turn it on in full-game runs and ILs), but state in the rules that full game runs should be submitted without milliseconds. If a runner does submit a run with milliseconds where they shouldn't, the verifiers can delete the milliseconds portion if necessary.