when i used to work at the local vw shop, we would always remove the precups, and machine them seperately from the head, when they are re-installed there should be no protrusion at all. rabbit on roids is entorely correct if you dont remove them the inconel becomes the high spot and screws up the machining on the head. not alot of shops will actually take the time to do them properly, i had the same problem on my 6.5, the guy in the machine shop left the precups in, and machined the heads on a taper. best place ive ever had a cylinder head done is eurohaus in alliston, been there for 40 years, and all he does is work on VW.