I was just finishing my first credo today (foraging) and it seems the bonuses to perception/exploration are plain increments to stats (like if given from eating/spending LP).
I think it's somehow penalizing players doing these quests early. My suggestion is that these bonuses could be counted in the same way as "equipment" bonuses (i.e., those given by gildings). This way they would be more "permanent", if you want

EDIT: and to do this, if it's not immediate to program, you might add some sort of "fixed" equipment slot (like, I don't know, "soul") that is updated with credo bonus (at least the numerical ones)