I've spent some quality time with the NF SAS, an SAS, a couple of 57/08 equipped guitars, and a 408 equipped Sig. Ltd. They're all cool, and they're all versatile. And all of them do things very well, but in different ways.
The NF pickup sounds different from the 408. So on the neck pickup, the choice depends on which you prefer. The 408 bridge sounds different from a 57/08.
In the end, it really doesn't matter how many tones you can get from a 408 or a Studio if you don't care for its tones in the first place. So it's really pointless to discuss which has more tones (i.e., which is more versatile), since they both actually have a lot of them, and both are very versatile. The real question is which pickups have the sound you like better.
If I were to describe the 408 bridge pickup, I'd say it's bright, modern sounding, fat, in 'bucker mode, and doesn't have all that much in common with the 57/08, which is the best rendition of a vintage humbucker tone I've ever played (including owning custom shop vintage style Gibsons with their rendition of their own PAF) So right there you have a big difference between the two guitars. In split mode, the bridge 408 is shimmery and sounds very "single coil" while a split 57/08 is less authentically "single coil" by design, but is a wonderful pickup anyway.
In the neck position, there's another difficult choice; the 408 neck pickup is a different sounding pickup than the NF. I'd say the NF is a rounder pickup with a more percussive attack. It has its own thing going on. The 408 can sound closer to a traditional humbucker, and the single coil sound is a little brighter, maybe has a bit less push. This stuff is hard to put into words!
The 2 pickup 408 guitars won't "quack," the Studio will. So if you occasionally want that phasey, funky quack thing, your choice is easy.
However, despite these descriptions, all the blabber in the world about this stuff is fine, but you still need to play both guitars and see which, if any, speaks to you as a player.
As to covered vs uncovered pickups, the covers affect the tone a little bit, so that's why they're there. But pickups are easily changed out, and PRS does make uncovered ones.