Starting skillpoints aren't really a thing in PF, so no, you won't get those. Remember, in gestalt you get the amount of skillpoints of your best class, so if your gestalt a 6+int class on a 2+int NPC class, you'd get 4 additional SP.
Oh, he got what he wanted to test exactly right. He just didn't quite think through all the consequences. The easiest way to test whether the definition for sewage encompassed everything was to use it to magically block off a pipe and check if anything got through. Of course, since the definition was correct, that meant there was nowhere it could go but back up into the workshop :P