I take mine to AAA to be verified. The last time was for the race car I just bought. The guy wanted to look under the hood so I let him. His eyes got really big when he saw the engine.
I asked him what he needed to see and he said he was looking for the emissions decal. I told him it was originally on the A/C box and that they had removed the A/C since it was a race car. He decided to mark it as missing.
Keep in mind the inspection that is being performed is to determine if the VIN and documentation match and that the car isn't stolen. It really isn't their place to determine whether or not the car has the necessary emissions equipment or the correct engine for that matter. On the other hand I wouldn't go out of my way to piss them off either because they could probably make things difficult for you if they really wanted to.
Neal