In the case of Zara's power, it could be that MC finds himself in a situation where he really wants to get down with a super horny chick but doesn't want to take the time to get undressed - so POW! he's naked and ready to roll.
But for most powers I think that if MC gets a non-passive power from a girl that would otherwise inhibit the further acquisition of other powers then his metagene dampens it and makes it controllable for him. If the girl can't control it but it's cock-blocking MC then he can dampen her instance long enough for him to acquire it.
I don't think the pill has anything to do with making the power passive; it's just another avenue to get the power if MC can't convince a girl to bang him or it's possessed by a guy. MC's metagene figures out whether having the power active all the time will cause a problem or not no matter how he gets it.