VFTs usually bloom in the spring. Most people cut the flower stalk off as soon as it is long enough to reach, as it does take energy away from the plant. If you let the flowers go the least that will happen is your plant will slow down a little on new leaf production at worst they could weaken it to the point it dies. The last is not very likely if you have a healthy established plant.
I'm not sure what you mean by using the flower (stalk?) as a seed unless you mean as a cutting, like a leaf cutting. I don't know if the stalk can be used as a cutting, but there's nothing lost by trying. There are a couple members on the forum who have had small plantlets sprout from the flower stalk as it bloomed.
I'll post the links if I can find the topics again (and no one else beets me to it).