I don't take credit for any of this sense I've heard others suggest many of these ideas.

Transcended necros should dodge DO in some way - either it ceases to exist because their divinity precludes them from a god-smiting, or because they can just re materialize themselves.
Actually, they should dodge all DO related effects, like no being able to be healed, shifted, HE, etc. Self shifting would make sense but I'm fine not getting that for balance reasons.
They should have access to holy spells given their innate divinity (still scroll only, that's fine.) Alternatively, allow them to change their effective attunement via some ritual or ritual spell. That would have the same effect but arguably be pretty cool.
They should have a fluff transcendence mode where they show off their divinity.
If a cleric perceives them, they should react to it in some way, because damn that's divinity right there.
Their Transcendental Buffs should have difference fluff messages - they should be less gross / demon based. It would be awesome for Zombies and Mud Men to look different as well.
No more need for a ritual knife, they can just bring about the ritual effects via force of will. I know we get a spell for this, maybe just re-skin that so that as long as it's "up" they can do rituals, but no gross bone knife.