Mmh...
Well, my wild guess is that the private room system is there for people not in a Free Company, and thus not able to have a house of their own on a Company Estate.
Where Company Estate houses will (supposedly) enable furnishing and such (the old Mog-House functions), they'll also supposedly allow for the structure itself to be modified and improved and changed, gardening, chocobo rearing in said garden, and possibly a basement for larger craft projects.
So I imagine that.. in their final, 2.0 form at the very least, Private Rooms will not be limited in what they can do, but simply lack the exteranl customisation/gardening/basement elements.