The stock setup relies upon the bolts bottoming out in their holes while the rubber crush washers provide the additional "push" on the gasket to seal it.
My ARP kit utilizes stainless shim/spacers between the head and the valve cover which allows torquing everything together rigidly. The spacers set the ideal height between the valve cover and head for the gasket to seal and prevent it from being crushed. The only caveat is the spacers are small and need to be placed with the utmost care... pretty easy though, I haven't lost one yet.