Same goes for monsters in subdungeons. Some effects do penalize them, others do not.
Items are also inconsistent. The benefits from the troll heart don't go away when you convert it, but the benefits from the trisword do, and you don't know what's going to happen until you test it out.
Mana burn prevents some types of regeneration but not others. Schadenfreude works, blue bead does not. On the other hand, life-steal does
continue to function even when you're poisoned.
If you take the Blood Curse boon from Dracul at level 9 (promoting yourself to level 10) you will not receive the ding max medal, but if you take it at level 8 (to reach level 9) and subsequently reach level 10 you will qualify for ding max.
Merely picking up a glyph and putting it in your inventory disqualifies you from "Warmonger" (as opposed to the text which indicates you just have to not use it). This automatically disqualifies T3 classes from the medal.
Jehora Jeheyu's Chaos Avatar grants a full heal and mana restore with level-up, unless you're already level 10 in which case it does not grant the usual full heal and mana restore from a milestone (but still increments your milestone count). Furthermore, unlike humility and blood curse it resets your XP counter and discards all progress made towards your next level.
Mystera and old GG forgive non-XP kills that normally anger them, but Dracul does not forgive non-XP undead that you kill.
Then there's the stuff that's just plain obscure, like the Reflex potion. Nowhere in its description text does it indicate that you may get two attacks under certain conditions.
Edit: The real problem with TT's desecration is that it's literally a game ending punishment. For him and GG, they might as well kill you like JJ does.
If you're not a first-striker and you use this boon to get a blood swell, protection, or unstoppable fury to land one last blow on the boss, then it works. It's definitely a desecration you don't use until the last moment. For GG... I have never actually desecrated him without agnostic collar. Way too steep.