You still dont get it do you ? The head face of a TDI is FLAT,so it does not matter if you skim it,its the thickness of the gasket that controls the bump clearance.The only area of the head face that doesnt get skimmed is the small area around the valve heads.There is a limit to what can be safely skimmed off the head,plus the measurement of the valve faces to head face needs checking and material removed from the valve seats if the measurement is too small.
The Head Gasket is chosen as a result of checking against the chart with the height of the highest piston protusion measurement.This should be checked every time the head is taken off,so you dont rely on the last bloke getting it right.The only time a different thickness gasket is used is if new pistons/rods/crank is fitted or if the block face is machined.
The gasket choice is as follows,
Protusion 0.50 - 0.60mm use a 1 hole gasket
Protusion 0.61 - 0.70mm use a 2 hole gasket
Protusion 0.71 - 0.80mm use a 3 hole gasket
Protusion 0.81 - 0.90mm use a gasket with no holes.
The protusion is best measured with a DTI,but can be done with a straight edge and feeler gauges.
So gasket choice is nothing to do with head skimming,hope this is more clear.Remember this is a diesel,lots of diesel procedures are very different to petrol engines where most of them have the combustion chamber in the head face,so skimming raises compression - hence needing a thicker gasket to keep the compression ratio the same and maintain valve to piston clearance measurements.