Sorry for the late response and unfortunately I can't help you with the Marr pickup comparison, but yes, the stock pickups are Fatter sounding than traditional jag pickups. I like them fairly well but prefer vintage type sound, so I am installing a set ofAV65 pickups in my 50th ann. Jag. If you get it, I would suggest trying the stockers and your preferred amp EQ first and swap them if you still feel the need.
Having said that, I absolutely love the quality, features, and playability of the 50th ANN Jag. As I said, I usually tend to prefer vintage sound and appointments, but the playability of this one is better than my vintage spec Jag. As far as the closer trem placement, I like it just fine and the better (IMO) playability and sustain. I know purists will say it impairs playing behind the bridge, but that is just not something I do. As far as affecting the "Jag" sound, I really don't think it is a factor any more than several other variables between individual guitars. Again, my opinion but also based on my experience over 50+ years of playing. Interestingly, I noted that the bridge to trem distance on my 50th ANN Jag is essentially the same as on my Gretsch Prolines.....so I don't think there is a right/wrong measurement - different strokes and all that!