FWIW, I do not have 'wipe with retract' on the machine used for this test: I've found if I'm using a volcano nozzle from .8-1.2, this has a large advantage in reducing blobbing from all the drool that falls out. But on .4-.6mm nozzles, not so much, and in fact, can actually make the print quality look worse in some cases, IMO.
But you bring up a good point: I've actually wondered (and not yet tested, although it would be easy) the same thing: If, in S3D, you have 'wipe with retract' set, but also enabled firmware retraction (via scripting solution of m101/m103) what would happen? Can you combine the two? I thought not, figuring S3D would be doing some sort of magic wipe/retract combo gcode, while firmware retraction (I presumed) 'just retracted', and had no concept of combining that with any other move at the time.