#1: The statue at the end(after you put the 3 skulls on the things) blocks the little tunnel you can go through. I'm guessing that in synergy the hit boxes are bigger than the ones in gmod(I think this was originally made for gmod).

#2: The 1010101 material at the end of that tunnel is an error. I would suggest to check the VMT and make sure the directory corresponds to the content you packed into the map.