Back in the mid 90's, the Navy paid for the contract to modify 45 KC-135Rs to the MPRS standard. Because of the limited amount of fuel being passed via the BDA (Iron Maiden), they deemed it necessary to allow more than one receiver to refuel and decrease the likelihood of a "sour" tanker. IIRC, only 27 sets of pods were delivered and currently the AF maintains 20 aircraft.
The Tomcat WAS refueling from MPRS and was very involved with the initial testing (as was the S-3). Wing clearance, flow rates, etc...
The reason you believe that most Navy aircraft refuel from the BDA is that there are simply more KC-135s without MPRS, than with. A BDA can quickly be mounted on a boom, as the mission requires.