I had this installed for a few days and realized that I'd never seen a Conqueror. Looking at the mod in both FO3Edit and the GECK I could see no reason it wouldn't be spawning them. But I did do a clean it up on it to Remove "Identical to Master" Records (there was one Form List that was removed) and, on my next Super Mutant encounter, a Conqueror appeared. I still don't know why that would have kept them from spawning so it might be a coincidence.
I just did a bit of bug fixing and hopefully this issue doesn't come up for others. Glad its working out now for you though. I will be merging this mod with another one soon - for all those interested. Its out lined in the description.
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Great addition to the game!