I don't know, in my game I found non-scripted gaia worlds and everything was normal. If someone else happens, tell me.

This issue only occurs when this mod is enabled, and it occurs even if this is the only mod enabled. I have tested for both 2.2.1 and 2.2.2.

In trying to narrow down the issue, I overwrote the mod and put all the other habitable world types into the mod file with their vanilla definitions. This resulted in all non-scripted habitable planets spawning in the same way that the non-scripted gaia worlds did -- no planetary features, just blockers.

Further, when this issue occurs, it seems that only three types of blockers are spawned on non-scripted habitable worlds: Impassable Mountains (d_mountain_range), Active Volcano (d_active_volcano), and Dangerous Wildlife (d_dangerous_wildlife_blocker). These also happen to be the first three blockers defined in 01_blocker_deposits.txt.

I can't find any good reason that this should be happening, but it is.

It should not, only the modifiers are changed, the rest of the file is exactly the same as the vanilla game. But I'll check to see if the same thing happens to me.

I believe this is causing non-scripted gaia worlds to be generated incorrectly at game start. They don't have any planetary resources, just blockers.

The overwritten files are 00_planet_classes.txt and 02_planet_classes_megacorp.txt, and only the corresponding part is those 4 planet classes.

Regarding the changes, I am open to them. The problem of the research bonus is that then the Machine World should also have it due to similar reasoning. It could also apply to each planet bonuses to specific resources, for example that the Gaia Worlds have a greater production of food than minerals or energy. The problem is that this could make the planets a real mess with a lot of modifiers.

Wonderful mod! What files exactly are overwritten? That helps check other mods for compatibility.
Also, I personally get the feeling that a world so completely taken over by a hivemind would be able to think better than a world with lesser density of drones.
Higher intelligence in animals is correlated with greater interconnectiveness in their neural system, and as hive mind building nomenclature alludes to neural systems, it would make sense for a hiveworld to be the central brain of the hivemind, with other research planets as smaller brains, similar to how cephalopods do this stuff (look it up, it's really fascinating!).
So, a small research bonus on a hiveworld? Like a +5% research boost and only +30% Defense Army Damage, and perhaps a small malus as well, like higher building upkeep?

It only overwrites the four modified planets, so in principle if that mod does not alter anything referring to these four planets then it should be compatible. But surely I do not know because I do not use it.

Is this compatible with Planetary Diversity?