As you know I used to work at Microsoft on areas surrounding cryptography, certificates, protocols and other such things.
While I can’t talk about the internal workings of things I can explain the high level roles the two sets of PKIs Microsoft maintains.
The first PKI is the Microsoft “Product Roots”; these are the keys and certificates that are managed with the sole purpose of being used for product scenarios. You can see the names and serial numbers of these CAs here.
The next is the “IT Root”, that is the one folks see associated with a S/MIME email from a Microsoft employee, some of the corporate websites have SSL certificates from this hierarchy and if you were to inspect the badges of an employee you would see a certificate from here that is used for smart card login and other related scenarios.
The “Product Roots” are trusted only by Windows and applications that have either built on the Windows CryptoAPI or simply imported the roots from the Microsoft Root Program.
The “IT Root” is trusted by third-party browsers because it has been cross signed with a public CA, currently that CA is Verizon the certificate is labeled “GTE CyberTrust”.
I hope that helps clarify for people,