Well theres certainly difference between different pole and slug materials and shapes. I cant comment on covers though - not had the opportunity to hear anything but there or not.
I can imagine theres a difference, given the difference in magnetic properties of the materials, but I dont imagine its bigger than the difference from totally slackening off the strings and retightening them between the pickup changes, and even with new strings each time, I dont imagine you could tell the difference with 20 minutes between hearing them, and it would be WAY smaller than the difference between guitars.
Non-issue. Covered or uncovered, yeah, a little bit, but this? No.