TC, here's a reason for killing the fruit before they turn into Seedlings, that no one here has mentioned yet : consistency.

You have to kill them before they sprout in the final boss. If they sprout in the final boss fight, those adds give a stack of that buff with each Melee hit. That's something to be avoided at almost all costs.

Contrast that to the fruit/seedlings before that boss, and you are rewarded for letting them spawn.

It's the only time I can think of (bearing in mind that I got up less than 20 minutes ago) where the dungeon teaches you a mechanic exactly opposite of what you need to do later on (in that very dungeon, no less).