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.
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Relates to MC-173180
Something similar happens with hoglins that ignore warped fungus that are planted over pots; they don't flee from them like they do when they are planted over nylium blocks.