As I understand it, you can do five things with plants:
eat them,
cook them,
brew them,
thresh them (at the farmer's workshop), or
mill them.
Cooking destroys seeds. Everything else leaves seeds.
On the fertilizer, I have no idea. The current game balance already seems to produce lots and lots of food.
Woops, forgot about milling and threshing. Since they aren't going to give you booze, and plump helmets aren't threshable and millable, brewing without cooking seems the best option, considering you can cook booze (even if it's not as satisfactory as cooking real stuff).
The quarry bushes not yielding seeds seems like a bug, you may want to report it or check the inventory of the farmer's workshop and the inventory of the farmer when you process them.
Also, cook the leaves if you aren't doing it already.
