For the planets, you'd have to make extra effort to make sure the Extra Huge planets and Stellar Moons remain in the game. I'm not sure if this would mean modifying the FQM files or not.
As long as the FQM STD secttype.txt and planetsize.txt files, which are just the stock files, are not copied over, those should be fine. Artificial planets are constructed via items in components.txt and the extra huge planet is still a "huge" sized planet as far as SystemTypes.txt is concerned.
I see that they are an ancient ruins tech. That ability needs to be added as a possibility to stellarabilitytypes.txt. But the actual tech, components, and planet entries should be fine.