I'd eliminate left over seeds from brewing and eating, it makes no sense, brewing is SPECIFICALLY the germination and fermentation of seeds which KILLS THEM, and people do not save seeds from every meal.
That's obviously true for wheat-oids but less straightforward for plump helmets or fruit, where the entire harvested plant is edible, not to mention wholly unexplained things like sweet pods.
Having to process plump helmets for seeds would suck, you'd have to destroy a large portion of your crop to get the tiny portion that's seeds. If they had a handful of spawn each instead of one apiece that would cease to be a problem but would create a lot micromanagement more work for the player. The current farm seed system is not 100% true to life but at least usable.
A bigger problem with crops as seeds is you'd never be able to have more than 200 cave wheat at a time. Just keep it around as cave wheat instead of seeds, have milling or brewing produce chaff instead of seeds, and threshing produce seeds and chaff.
But
that won't be practical until we have a better way to control threshing and milling. At present I must grow dyes, sweet pods, and rope reeds in different seasons to get dwarven rum and thread instead of dwarven sugar and river spirits. The kitchen menu really, really needs MILL and THRESH options alongside BREW and COOK.