So after discovering that overrides sometimes nerf gear I have decided to check all of my own override gear to find out stat discrepancies, here is a list of gear nerfed or changed stat-wise by cosmetic overrides. that I currently own.
The turquoise slayer helmet removes the +3 attack bonuses to magic and ranged that the full slayer helm normally gives.
Imbued Praetorian top + helm (t2) are both missing the bonus hp from the Virtus they are imbued with.
Overriding the Staff of Eternal Hellfire (t2) with a Shard of Ice reduces it's slash attack bonus from +5 to +4 (this is really only continuity).