Imagine this: Our Heroes need to sneak past a guard and want to be on the safe side, so they ask the party's Grey Wizard to cast Bewilder on him, using the conversative side that gives the target the perplexed condition. The spell succeeds, and the players make their Stealth checks opposed by the guard's observation, and since said guard isn't actively looking for anything, he won't get to make a check himself.

The problem is that even though the spell would have a quite cripling effect on his mental abilities, it only affects his checks and thus does nothing insofar as he plays a passive role.

Similarly, using an action that targets someone's Resilience won't be any easier if the target is Overwhelmed , and I don't think that's making any sense.

Could any of you help me make sense of this, or perhaps offer a solution to this problem of apparent logical insonsistency?

You could just give the players a few white dice as a bonus for "good conditions". Or you could roll for the guard as most guards should be on the lookout.

In that situation, I would apply exactly 1 white die to the roll to represent the condition. To my eyes, the rules seem to imply that's how it works.

Per pages 50-51 of the Player's Guide (and again on Pages 76-77 and 83), the GM is always free to add fortune or misfortune dice to a pool to reflect the task being easier or harder than normal. Typically you add 1 white or black per miscellaneous advantage or disadvantage the character has.

If you look at the opposed check rules (Player's Guide, page 52), you'll find another precedent implying this is the way to do it. Skill training, specializations, and A/C/E all generally add white or yellow when used for an action, but if used by the target of an opposed check they add an equal number of black instead. The implied converse of that would be that if there's anything in play that would normally penalize the target's actions by black or purple, it should probably add an equal number of white to the active players opposed check instead. It's not technically official, but it's certainly in keeping with the spirit and implications of the rules.