My only valid solution for this: Limit valid growing space, then collect the seeds as needed.
As a small gift, for some people, here are a few odd seeds and how to show up...
Rain Seeds can be planted by raindrops during the rain, so they're odd(same with lightning seeds, they can be planted when lightning strikes a area).
Slime Seeds spawn slimes when they grow, as do Squid seeds, but they both have a chance to be dropped by their respective mobs.
Potion seeds make a splash potion effect, and that ends up with at least one new seed, but they can grow from nothing if you make splash potions and throw them.
Helium Seeds float up and root themselves to netherack roofs, so keep that in mind.
Ender Seeds can show up when endermen teleport or the player used a ender pearl(maybe eyes as well, not sure).
Fire seeds can show up when fires are started(no way!). Careful growing these things, though. You can guess why, yes?
Creeper Seeds are weird. They show up occasionally when a creeper explodes, but they prevent the creeper from doing damage when this happens. They polinate by shooting out a seed, like most other plants.
...Point is, all seeds/plants grow under unique situations which are pretty cool.
As for harvesting them, that's easy, you need a good tube system and it has to be able to rapidly enter a vacuum state.(0 BAR at the drop of a hat, or able to maintain this level easily even with some atmosphere entering your system)
You'll need air grate tubes for this, and of course a way to store them when they enter your system through those tubes. Eventually the plant will enter a seed emitting state, and it will do something. When this happens, if it's a rain seed, it can make it rain AFAIK, and lightning seeds can only be planted when lightning strikes, so I assume they can make rain into a thunderstorm.
For seed/slime seeds, they make a new mob, and then you need it dead and hope a seed shows up from this.
Almost every other seed spits out a seed in some way, that's why you need those air grate tubes and a strong vacuum system, to suck up those seeds before they land, or if you have a limited growing area for them when they do, and they you collect them as you wish. With the exception of fire flowers, helium seeds, squid seeds, and ender seeds, everything grows on dirt, grass, or farmland. Squids need water, fire flowers and helium need 'rack, and ender needs, you guessed it, end stone.
