I actually had to get a bunch of gunk out of the bolt holes because the first time I installed it, it wasn’t flush. But once I did that, everything went on smoothly and laid flat. If the thermostat is off center, would that cause issues?
Can you post a photo? It shouldn't move much the the bolts partially threaded, but I've never had one of those fancy billet pieces. I guess I've just been lucky with all of the stock housings I've installed.