On your engine the pistons are down the hole 3.15mm to 3.6mm at TCD but that is not typical. Usually the piston is a small amount out of the hole. Looking at the manual it varies from .1mm to .75mm (.004" to .03")depending on the engine.(except for the 117.981 to .984 which is yours) so I can see how you would wonder about achieving .040" of clearance.
BTW the 5.6 pistons do have a 30c dish. You are correct-if they were flat the CR would be WAY too high. The area around the dish is flat and creates the squish area.

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Tony H
W111 280SE 3.5 Coupe
Manual transmission

Past cars:
Porsche 914 2.0
'64 Jaguar XKE Roadster
'57 Oval Window VW
'71 Toyota Hilux Pickup Truck-Dad bought new
'73 Toyota Celica GT