I suspect they made two different models because MK wanted "his" shape, which to me is not ideal for 22nd fret access, and the NF 53 shape is "more classic-ish" shaped. As I noted elsewhere, the NF53 neck has upper fret access similar to my Squier Tele.
The pickups are not the same in these two models. NF 53 has "NF deep dish" pups, which have pole pieces that are (according to PRSh) half the amount of magnet that goes into a regular pole piece, but squished into an elongated rectangle, and could have more windings (and are deeper, thus the name). The net result if you listen to the demos is that the MK sounds more like a NF HB (fatter, higher gain), whereas the NF 53 sounds closer to a SC tone, but without the hum.
Switching is different. Neck thickness if slightly different.
Aesthetically, the shape is different (aside from fret access), and the pickguards are different.
So they really are two different guitars, that both happen to look like T-types.
I think PRS was aiming for the NF 53, but MK said "I want this and that differently", so PRS said "OK, two different models, let's not market just what MK wants".
I suspect the MK will go away after a few years, and the NF 53 will stay, but pick up a few of the MK features (like the pup single coil modes/tapping/whatever).