The plastic covers are chromed inside and out so pretty easy to peal it, the epoxy does not stick real well to chrome. Just a block of epoxy with a wire sticking out. The big difference might be getting the pickup closer to the strings? The bass just sounds brighter now not microphonic. The plastic is about 1/16" and there was another 1/16" of some kind of glue holding the metal covers on. The metal covers are about half as thick of material than the plastic covers. I also put a little foam under the bridge side of both pickups to get them to set parallel to the strings with the 2 hole covers.
Aha! Pretty sure the difference is related to removing the metal covers...are they steel (very magnetic) or nickel silver (slightly magnetic, your new covers are made of that. Steel is used to spread the magnetic field, a good idea with the slug magnet Artecs and also to shield the coils. Seymour Duncan uses metal screen to do that. Your new NS covers do a similar thing, providing a shield and affecting the mag field. They also 'sweeten' the sound. ThunderBucker could explain it more clearly but that's the best I can do.
Getting the magnets closer to the strings also has a huge effect on sound, emphasizing treble over bass.