Only "Faction" guys.
Latest dev build(Build by myself)
1341904

It seems that the other entities is not added to ForgeRegistries.ENTITIES

That is all ForgeRegistries.ENTITIES.getKeys().stream().filter(resourceLocation -> resourceLocation.toString().contains("ancient")).collect(Collectors.toList()) entities

I am unable to replicate this in the current released version, and we don't really support issues when you're building the mod yourself.

I think the faction save with nbt is terrible to normal player

That is a decision by design, instead of registering hundreds of unique entity IDs we define it via an NBT tag. The "normal player" is someone who plays with this mod as is.