I have a Customer that uses different PCs registered to different MS Active Directory domains (with no trust between each other) on the same LAN.
I know that ISE can connect up to 50 isolated MS AD domains, but I would like to confirm that this is correctly handled in SDA fabric and there are no caveats on this kind of config.
Not exactly sure what you mean by "transparent". In general, authentication (via AD or any other identity source) is separate from policy. You can however based SGT assignment based on which AD group the user is a member of.