Bart, to answer your question:
When dealing with a quench head/piston arrangement like a small block Chevy, yes, you can pop the piston crown out of the bore at TDC and use a little thicker gasket to achieve your 0.035" to 0.040" squish. You can also achieve the correct squish with the piston slightly down in the bore by using a thinner head gasket. For instance, I saw a 0.016" gasket sold by Chevy. With that gasket and the piston 0.024" down in the hole, you'd have your 0.040" squish. Or, like I say, if the piston was popped out by 0.020", you could use a 0.060" gasket to achieve your 0.040" squish. Hope this helps.