The motoryachts with an Aft Master Stateroom typically have a mid-engine room layout with some long shafting and additional struts/bearings for support. Putting the drives in the current propeller location would have them underneath the Aft Master Stateroom berth, which usually has water or some other type of tankage below.
I could picture a neat, pre-engineered copckpit extension including pod drives layed up ahead of time, and then mated to the exitsting hull with not that much of a struggle, keeping the propulsion machinery out of the living spaces and allowing for new uses of the old machinery space.
Just thinking out loud......
