Mountain Lion Server is a lot more self-sufficient as an app than it used to be. Not only do you no longer need the Server Admin and Workgroup Manager applications to manage the server, but the Server app actually has a faux root for the tools that were once distributed almost haphazardly across the rest of the file system. These objects are now stored in a faux root, where /Applications/Server.app/Contents/ServerRoot is the path to the faux root itself.
If you need to access any command line tools, they are relatively placed to that path. For example, if you’re experimenting around with Profile Manager and need to wipe the database with the WipeDB script, that’s now stored in /Applications/Server.app/Contents/ServerRoot/usr/share/devicemgrd/backend/WipeDB.sh. Meanwhile, serveradmin, one of the more useful tools is stored in /Applications/Server.app/Contents/ServerRoot/usr/sbin/serveradmin. Some tools, such as slapconfig are also a part of OS X client, so they’re still in their original spots (in the case of slapconfig, at /usr/sbin).
Overall, this move makes OS X Mountain Lion Server a bit more self-sufficient as an app and allows it to adhere better to Apple’s development best practices. While the paths will break some scripts, that’s some pretty straight forward stuff to fix.
Finally, the path for actual service data is still customizable. Click on the server’s name in the Hardware section of the server sidebar (from Server.app) and then use the Settings tab to customize the location of Service Data.