Vegepygmies and russet mold were introduced in S3 (Barrier Peaks). The mold was an alien specimen that had mutated and infested some of the ship's crew, converting them into vegepygmies. Through the editions, the methods of their reproduction have changed. In the first edition, the mold caused people to become 1-4 hit die 'pygmies (a percentage roll found in the MMII). In the Monstrous Manual, those converted by russet mold become 5 hit dice 'pygmies. In the Tome of Horrors (and Glades of Death), the mold produced 1 hit die 'pygmies. Also in the first and second editions, the plantmen could also reproduce by budding (producing 1 hit die version) and in the second and third editions the chiefs could produce spores that made 4 hit die versions. I had to take notes because it got a bit confusing trying to remember what was where as they are similar, but not quite the same. And it makes no sense that they lost their ability to bud in the third edition. I am thinking it was a simple oversight by whoever did the conversion.

Personally I like the 2nd edition version. The vegepygmies can produce buds that result in 1 hit dice members of the tribe and russet mold kills become 5 hit potential founders of new colonies.

But there is something lacking, a result of their origin (being a alien mutation). 'Pygmies do not farm, culture or otherwise pay attention to the mold. They don't provide any benefit to the mold either. It doesn't spread because of them and thus it is pretty much stuck in very limited locations (crashed starships and maybe planar gates). That is easy to fix. Just add a racial trait that states that dead vegepygmies turn into patches of russet mold unless they are exposed to conditions that would kill the mold (sunlight mostly).

There is also the question of why plant people are restricted to dank forests, the occasional dark swamp and underground. That is another easy fix- they dehydrate easily. Wind based spells do them damage at d6 per level or, for those that already do damage, double the existing amount. Those underground survive by eating meat (which is mentioned in every edition) and fungi (which is only in S3).

Thornies, dog like plants used by some vegepygmy populations, have no origin mentioned anywhere. They are found in one of the two colonies of 'pygmies on the ship and I would guess they are either converted pets (doubtful), another mold culture gone wrong (possible) or alien plant life taken aboard the ship in its travels (probable). What I would do with them is have the 'pygmies carry thorny seeds with them when setting up a new colony. They would be easy to grow as long as they have access to some light and meat. This obviously restricts their use underground (though not completely as there can be glowing crystals or other light sources).

There is also mention of how well they work with other plants- though only shriekers are mentioned in S3. Adding in violet fungus (really evil in 1 and 2e), zygoms, phycomids or some of the other fungal monsters and deadly plants in the 1e MMII (mostly from S3) and updated in various books in 2 and 3e would give the colony a lot more flexibility in their defenses. And of course, there should be russet mold colonies. The intelligent version of yellow mold from 1/2e can be incorporated into the russet, thus making it a psionic monster as well as potential leader/god of the 'pygmies.

The big question is where did the mold originate? Is it an alien? For settings without planar access or aliens, who created it? Druids or wizards wanting a method of reducing humanoid populations ('pygmies are more powerful than most of the basic humanoids)? A fungal demon or god wanting new worshippers? A chance mutation like in S3, causing a potential pandemic of vegepygmies throughout the Underdark? Would that be a good thing or not? Or is it something very different? Some real fungi have four different forms (sexual, asexual and two host species) and russet mold and vegepygmies can be incorporated into the lifecycle of other fungal and plant creatures. Kobold Quarterly did that for the phantom fungus (adding in migo and some rather nasty superfungal monsters) and it should be easy to do here. May be they are part of a dark secret for treants? Eh, there are enough other plants and fungi out there to avoid such a senario (treants are meant to be forest herders, why the heck would they have a fungal monster in their lifecycle?).