The railcraft componentworkshop does not generate a foundation like the default village worldgen buildings and will sometimes float midair or on water. The first two screenshots are of the issue. The third is of one of my shops using the functions in StructureVillagePieces to generate a foundation. I recently fixed my worldgen buildings and would gladly submit a fix for this issue if you'd like.

Fixed by #669

Submit a fix but dont forget the (CLA){https://www.clahub.com/agreements/CovertJaguar/Railcraft)