I figure I never replied to this; I think for unique seeds it's healthy to extract some from harvested fruits and keep them in a safe place; I don't think we are ensuring all unique seeds are being generated tho, that's something we should look into.
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yeah, I figured it's not that important for early access, but I've definitely had issues where I've only had one of a specific seed spawn, and then an animal got to it before I could harvest and replant. been less of an issue since I started being more careful, but it does leave you in a weird state where you can end up with runs where you just can never complete the journal but also you don't lose.
something like having the game check if there are any plants with no plants/seeds in the world, and then giving a chance of animals dropping them for the day could be a solution? just an idea though! I think it's also fine to just accept that sometimes you get all the plants and sometimes you don't! :>!