It used to be that the biggest reason to keep them separated was for the LiveUpdate policy/schedule. Since Macs can only get content updates via LiveUpdate, it was a good idea to keep LiveUpdate enabled and scheduled, but you didn't necessarily want that for the Windows computers. Settings were not separated by OS type.
With 12.1, the LiveUpdate policy has a separate section in the same policy for Macs as for Windows, so the same policy can be applied to both types of computers. The Windows Settings only applies to Windows computers, and the Mac Settings only apply to Macs. (See attached image.)
If you want to keep them separated for another reason, then that's perfectly OK. :)
sandra