I'm always swapping mags to go into PRS guitars....it's easy to reverse, as long as you're careful!
On its own the tone of the neck will be unchanged, together you'll get the Greeny tone.
Covers tend to roll off a little bit of top end, just a touch. You can get them uncovered, if you like then great, if you think covers will get you closer, send them back to Tim for covers putting on, he'll only charge for the covers and postage. Try and get Seymour Duncan to do that!!