Bees will go towards and pollinate flowers that exist placed within the world, however they will not go near the exact same flowers if they are inside of a flower pot.

This could be fixed by switching up block tags - for example, a #bee_pollinatables or something less awkwardly named that bees path to for pollen, by default containing #flowers and #potted_flowers, #potted_flowers that explicitly only contains actual flowers in flower pots, and #flower_pots could be reduced in size by including #potted_flowers.