Most Velux windows are installed from the inside. Basically, clear plaster board around the area, lift tiles from inside, cut and reinforce the roof timbers, then lift the frame into position from the inside and fix. You then make good the tiling and lift the glazed frame into position again from the inside. Finally making good the inside plaster work.
Not sure on the planning aspect, but if he needed planning permission, so would you.
Personally, I would suspect the job got forgotten during the build and it will cost much more to rectify the error at this stage - hence the attempt to get away with it. Stick to your guns!