I've been using Pi-Hole happily for quite sometime now in our Windows Active Directory domain.
The setup is as follows
client → Microsoft DNS → Pi-Hole → OpenDNS
This works great since AD authentication is working as designed and clients can find all the required srv records in the Microsoft DNS.
Up till now the only drawback was that I could not see who did what query but that was not a huge issue.
With the release of the 5.0 and the client and group based exceptions I would really like to be able to get my setup like this.
client → Pi-Hole → Microsoft DNS → OpenDNS
I've already tested with it and configured as follows
Custom Upstream DNS Server = internal Microsoft DNS
This is giving me authentication problems on my domain.