There's a bug where the greenhouse terminal doesn't acknowledge the existence of seedlings in the deposit unless I first select an empty planter slot.

Is that a bug? I thought thats how it was supposed to work.

Select the planter you want to use > select the plant you want to put in it > and confirm

Exactly this above OP - YOU have to plant seedlings. The game wouldn't automatically do it for you because you have limited seedling space and it's up to you to decide WHICH seedlings you want to plant.

Different species of crew breath different biosphere - and each seedling provides different biosphere (some are even better at providing the same biosphere - so you might find a seedling that provides KOH and another that provides 2 KOH so it's twice as good).

If you want to lean heavy on one or two species you won't need much of the other biospheres - if you want a varied crew you might need to invest in several different types of seedlings.