Dan, I can't really comment on MXY's, but I can give direct comparison between two very similarly constructed Alembics. My Custom fretless 5-string was built around the critical specs of my Persuader 5-string. (remember that one?) Both have the 32" scale, 3 purpleheart neck laminates, mahogany body core, and maple tops. The electronics are similar too, though my Custom fretless has an added bass and treble boost/cut.
What's different is the pickups themselves. The '89 Persuader of course has the stock P/J set. (new replacement set from Alembic in 2014) The '17 Custom has an AXY in the neck position and am AXY 'FatBoy' in the bridge position. Both pickups are offset from the extremes by 5/8", which places them a good ways apart.
These two basses sound
remarkably similar. In fact, I can make them sound indiscernably alike. But I'm not so sure it has that much to do with the pickups. I think it's a lot of things... the placement of them, the inherent nature of that P pickup and its
location on the top, the electronics, the strings I use, (TI Jazz Flats on both) just too many variables to list.
All things being equal though, I have two Distillates, a fretted and a fretless, made within a couple years of each other, though one has a walnut top and the other, bubinga, their neck recipe' is the same, they are electronically identical... and they sound
nothing alike. Go figure.
FWIW, I don't think there is a huge difference in the magnetic properties of MXY's vs. AXY's... I seem to remember reading here somewhere it was a matter of accomodating the wider string spacing. I'm less sure how they stack up against the Fender-shaped pickups. Hope some of that rambling is helpful.