Yes the o-rings "compress" in that they distort to fully fill the square o-ring groove, so the head height does not change either way. Take caution using solder as it can potentially become cut by a port and become destructive debris.
So what would the proper squish clearance be on a yz125 with PC pipe and silencer, 38mm Lectron, running a 50/50 mix of VP110 and ethonol free premium mixed at 40:1 with Motorex 2T