Been awhile since I played ES2, so I missed a few versions of this mod.
Enrollment got changed from a flat 300 manpower in Vanilla to 150+bonuses you get from various building. So far, all clear. Encourages you to take a hero skill or build some stuff if you heavily rely on that way to get manpower.

When using it with the Riftborn though, it does not add any(or very very low? like 1.5 instead of 150) manpower at all.

Is this intended or a bug ?

If intended (maybe Riftborn are supposed to not have that feature anymore ?), you still lose the minor pop/-300 food, and still cant use it on pure Riftborn pop systems. So maybe there is a way to deactivate it with minor pops on a system as well to make it more clear it's not available for Riftborn ?
If a bug, happy squashing !