Since they both come from bees?
First, pollen doesn’t come from bees, it comes from flowers. The bees act as an intermediary to transport the pollen (which are roughly analogous to human male sperm cells) from the male parts of one flower to the female parts of another.
Second, the pollen doesn’t get used in making honey. The bees inadvertently get pollen on them while taking nectar from the flower, and then the pollen is removed from the bee when it goes to the next flower. Only a few stray grains of pollen might stay stuck on the bee when it goes back to the hive, and those wouldn’t get into the honey.
Beekeepers look at the pollen grains trapped in the honey to identify what flowers supplied the nectar, so I would assume at least some pollen makes its way into the honey.
Also, people are not allergic to “pollen”, they are allergic to one or more types of pollen. For instance, my older son and I are both allergic to birch pollen. Different kinds of pollen are common in different seasons. Around here, tree pollens come in early spring; grass pollens start in late spring and continue throughout the summer; and weed pollens go from late summer through autumn. Someone unfortunate enough to have an allergy in all three groups would be miserable for much of the year - but it’s three different allergies, not one.
I’ve never had the least bit of trouble with honey. The little pollen that’s in it gets destroyed in the stomach pretty quickly, I would imagine.