Wouldn't a poisonous liquid be a better option for them? The only poison clouds white Pikmin encounter are the ones they're sent to charge at.
Also this is the best mod idea ever and I want to subscribe to your newsletter. To carry my useless opinions to how the Onions should work, I'd go down the route of them being a building as well. I'll let someone else come up with a good way how to balance that(although with the mortality rate of pikmin without a leader, who needs balance when you could create a horde) but anyway...
A reaction to turn corpses into pikmin would seem appropriate, one way to accomplish it would be something along these lines.
- Corpse taken to Onion, processed, it creates a vermin named "*color here* pikmin sprout". Also creates a speshul stone that boils in room temp, and causes a syndrome on the vermin creature, that causes it to mature to a pikmin a few days later.
The bad thing about this is that the vermin would be able to move any way it liked until it matures to a real-size creature. Unless IMMOBILE tag works on vermin. Also those stones would be eligible as building material for slabs during worldgen as far as I understand, which might cause hilarity for a pikmin adventurer who wants to be a necromancer, but the slab has boiled away the moment you enter the tower area.
I can't really think of anything else for the building-Onion method. The domestic pet one... well it would work, somewhat, but would a caste member that's also a PET&DOMESTIC require to be married to create offspring? Not to mention that it's not exactly faithful to the source material that Onions like that would pop out pikmin once a year(is 1 year of pregnancy a thing that applies to everything or is there a way to edit that somewhere?).
Then again I don't think you can specify on corpses that would be taken to the building-Onion either, as far as the game is concerned, any body(or body part) is equally a corpse, so a tadpole(or what were those called again) would net as many pikmin as a bulborb.
EDIT: My mistake, there IS a different tag for corpses and body parts as far as reactions go.
EDIT2: Also as an opinion on the "natural digging ability", I wouldn't bother. Digging is easy to level as it is, and there's no way to make a creature that's able to dig without a digging tool in it's hands(or hand-analogues).
Also on the yellows that lack something special right now, make 'em a bit faster and better at agility in general than other pikmin?
EDIT3: On the planting thing you brought up, it doesn't work like that. A plant you pick up doesn't have a syndrome or reaction of it's own that'd magically make a creature, although it's possible to make that picked up plant cause a syndrome when consumed.
Although pikmin only eat nectar. So yeah.