Commendations and other bonuses are sorta perpendicular to stat caps: they just add a fixed amount to the stat regardless of what's happening with stat caps. Some commendations (Gun Kata is probably the most notable) do give you a boost that's capped by max stats, but that just means you should take this commendation before maxing your stat, or you'll waste the 'free' stat points. You never lose out on max stats via commendations as such, short of not gaming the 'Master of' and 'Bane of' commendations to get one of each level of commendation via different weapons/enemies.
Most XCF commendations actually don't really care about "allow above maximum results" and "upper bound mode", since it's not the commendation that increases the stats, but rather the associated soldier bonus.
What loses you potential stat maximums is the random stat gain when you hit the stat caps in the field. If you hit it via other means (mostly 'soft' commendation boosts like Gun Kata, but theoretically also training), you don't get to roll over the nominal maximum.
