Yes the guys are right, head gasket thickness is determined by the piston protrusion above the block. You should clean the piston tops and use either a DTI or depth micrometer to measure the depth.
If you had a factory car with 3 hole gasket this would simply mean that the surface of the block required slightly more machining to clean its surface, or maybe it didnt require it but thats what it got. When your dealing with cast iron and a face mill 12" in diameter... 0.1mm here / there is a reasonable target, compared to machining the likes of alu. in a CNC mill in which case you could quite easily hold a tolerance of 0.05, not +/- 0.1
Skimming an IDI head will increase the compression very slightly, as your removing material from the prechamber but also the recesses around the valves, but you dont really need to take this into consideration. On a DI the compression would change even less. Some engine builders would simply supply the thickest gasket to lessen the chances of a mistake, but if your car left the factory with a 1 notch, you had the head skimmed and you fitted a 3 notch, you would notice the cold starting ability change.
On the mk2 GTD I rebuilt (1.9TD), I only needed a 1 notch gasket, but because I wanted to run higher boost pressure, I installed the 3 notch and increased the boost to 1.5 bar. The car was no problem to start from cold with the glow plugs, but when warm it would turn over a bit longer than the others. No big deal, but it was noticable. You could always make adjustments to have the glow plugs operate above 70C.
When where on the subject, how does everyone feel about lowering compression when raising boost ? Most diesel manufacturers do lower compression slightly on turbocharged engines, for example Perkins engines used in agri. machinery, but how about the Finns who build the 350 - 400 HP Mercedes W123's and W124's (190 / 300). They run OM606, 3 litre straight 6 IDI's with compression of 22:1. Able to bring a turbo as big as a Holset HX40 to over 2 bar !
DM