Hmm, I have no experience with Active Directory Certificate Services, maybe someone else can provide first-hand experience. Microsoft has a history of ignoring standards (like how Active Directory differs from the X500 LDAP standard), so you are right to be suspicious, in fact the ADCS pages have no hits for "X509". These are questions you should ask Microsoft directly (or whoever your middle-man software vendor is).
In general: Almost all CAs / browsers / S/MIME applications / VPNs / etc use the X509 Certificate Format. This is a widely accepted binary format for certificates and public key information, and should be supported by any application / operating system that knows about SSL/TLS, or S/MIME.
I've worked with commercial-off-the-shelf CA software that can be hosted on any of Windows, Linux, HPUX, Solaris, etc and happily handles cert requests from any of the above + Mac, Android, iOS. As long as they all use the same network protocols and certificate formats, it shouldn't matter.