For two reefs or two FOWLs, I would say definitely plumb together. But when its 1 of each, IMO it makes more sense to go separate. For your reef, your going to want to keep your levels right, like calcium and magnesium. Your going to have to dose more to get those targeted levels, which will cost more, when you could just be dosing for the reef (at half the water volume) if you have them separate. For the fish only, its likely you'll have a lot of fish in there, and diseases will be a primary concern. Medicating the FOWL with copper could be lethal to the reef, and keeping ICH out of the system will only be harder in the reef with a FO connected to it.
Of course there are Pros to conjoining the system, like stability. Tank parameters seem to fluctuate more smoothly and less obstructively with more water volume.
Its your choice. But those were just a few reasons I would do them separate....