The freqencies carried through "bones in the head" are mainly the low ones. Low notes in isolation can vary quite a bit and sound in tune. But your voice also has higher harmonics/overtones, which are more sensitive to matching pitches, and which you aren't hearing.

Fine tuning is done with those higher tones, which you can hear better externally with the cupped hand.

Even singing solo, if you start out in tune with yourself then muscle memory can carry you through pretty much in tune.