Strangy, to measure valve/crown clearance you need to know the piston protrusion. All gasket thickness are based on this initial factor.
Machining the face of the head may or may not alter the requirement for next thickness and therefore it must be measured to maintain the correct CR in the engine also.
Quite often head machining will also involve valve seat recutting which then increases the valve/crown clearance resulting in the use of the original or lesser thickness gasket.
Using a thicker gasket for just any old reason will alter the CR of the engine quite marginally.
The only time the whole gasket thickness needs to be considered is in the event of any bottom end work as you said, but you still need to maintain OE tolerance valve/crown.
As alloy heads on diesels generally have a minimum machining limit based on the surface hardness of the face, this is generally less than the overall critical value required to cause valve contact with the piston.
Also, increasing the gap with a thicker gasket will allow a higher carbon buildup on the crown of the piston which will eventually result in face contact. Being a direct injection, all combustion is done in the combustion bowl. Increased gap causes a burn above the bowl surface which also reduces power and increases EGT's.
The clearances must be kept as close to original tolerance as possible.
As for TRS, I would take what they say with a pinch of salt. They aren't engine builders and definitely not diesel certified. They sell "stuff" and that's about it.
As for cam clearances, don't know how you came about the info but it makes absolutely no difference to the timing chain etc etc particularly with an 8thou facing.
I've worked on everything from KT50's, Wartsila V16's right down to lowly Toyota L series and have never seen an instance or supplied components where this results in incorrect cam timing.
Cheers
Andrew



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