This is an interesting contrast to my experience, the wiring on the guitar you have your mules in is a straight-up split? No foolins with resistors etc? I find the tone to be obviously different when split as well as output decreasing.
Ah, I've had a brain spasm! I've got series, parallel and coil split options on this guitar. I was thinking of the series vs parallel options, which sound remarkably similar (same volume, with the parallel option having a tad more treble).
The coil split does indeed have less volume. But the PRS has the biggest drop in volume I've ever heard from a split humbucker.