Guidance modifies the target number as opposed to the roll, the same way all bonuses are handled. There is actually a bug here which attribute test without a skill aren't affected, when they should be (technically there's no such thing as a skill check in 5e, just attribute tests with proficiency bonus).
Yeah, this is why Bards get their Jack of All Trades bonus to Initiative rolls. Initiative rolls are ability checks that don't have proficiency, thus they get the half-proficiency Bards get to non-proficient ability score checks.
