I've ran a few quick tests with a few mods that can tweak skill levels to see if I can find any incompatibility, and so far I found no problems!

Vanilla Storytellers Expanded - Winston Waves
Skill increase rewards still work, but they cap at level 20
ESCP - Skyshards
Works exactly as intended, a strength 5 skyshard will make a skill level go from 120->125 with no issues.
Vanilla Skills Expanded
No incompatibilities found so far.
Matrix Rimloaded (Continued)
The Skill Hack ability works like a neurotrainer, so it gives a set amount of xp, negligible on higher levels, but still works fine.
Character Editor
Has no problem increasing levels past 20, so I guess it's fine?
Biotech
Skill changing genes seem to work fine, they still reduce/increase when applied to a pawn with high skill levels