The main reason I'd keep theocratic clergy is for theocracy vassals, which have much higher obligations than feudal/city vassals, and don't have an opinion penalty for being at said high obligations. Do leased temple holdings give you bonuses other than a minor amount of gold per month? I haven't looked into it too much, but that was all I saw, and it wasn't very impressive.Warmonger and Communion are great combination, but to be honest I think Theocratic is much better since you can have leased temple holdings giving you bonuses
Tyranny reduction from Pursuit of Power is also great, especially if you combine it with other source like Bidaic holy site or Aachen Palace special building, in that case you can pretty much imprison/revoke anyone at will.
Your way of dealing with heresy is interesting, but to be honest it's not worth it. Heresies are just annoying 'what-a-mole' things. When they happen I simply imprison/revoke heretic vassals and that's it.
The tyranny reduction on PoP is indeed nice, although there are ways around most tyranny gains in this game if you get creative (e.g. revoke a vassals land freely by granting him as a subvassal to a wrong-religion vassal, then revoking all the wrong-religion vassal's land). I do agree it's still a nice-to-have though.
The dedicated vassal religion thing isn't to deal with heresy per-se, that's just a nice side effect. The main goal is to prevent vassals from converting counties to my religion, which cuts into fervor generation that I can spend on GHWs.