Michael Schlenker <[email protected]> added the comment:

It probably is even worse.

The flag seems to specifiy the physical locations, and just using 
CERT_SYSTEM_STORE_LOCAL_SYSTEM probably misses the certificates distributed by 
Group Policy or AD too, in addition to the stores for the current user.

See 
https://blogs.msdn.microsoft.com/muaddib/2013/10/18/understanding-and-managing-the-certificate-stores-used-for-smart-card-logon/

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