I'd say the best benefit is that the Explorer parts are much easier to come by than the Mustang stuff. It's 10 years newer in the junk yards. The OBDI Mustang stuff is starting to get expensive over the internet. Making a stand alone EFI system, using the Explorer based OBDII, you can also use it to run the 4R70w trans. Not having to buy an Optishift controller for that would pay for an Explorer harness and flashed computer, from EFI guy. If your wanting to upgrade to a 5.0 EFI, there's a lot more 5.0 Explorers out there than 87-93 5.0 Mustangs.
Mark