It looks like WinHttpCertCfg.exe is being used here . This is a cleaner way to set permissions on the private key of a certificate than the method described above. I assume that in Windows 2008 and beyond, MS decided to hide the keys in a more discrete place.
I used WinHttpCertCfg to set permissions. Here is an example command to provide read permissions for the NETWORK SERVICE for a certificate named MyCert01 in LOCAL_MACHINE \ TrustedPeople.
winhttpcertcfg.exe -g -c LOCAL_MACHINE\TrustedPeople -s MyCert01 -a "NETWORK SERVICE"
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