Okay so this might seem like a really dumb question, but I've always preferred the look of a shining chrome humbucker cover to a regular single coil, aesthetically at least. I'm going to replace the pickguard on my strat to a Black Pearloid but I thought I might be able to cover my pickups with a just a humbucker cover anyway.

I'm going to put a Dimarzio Chopper and Bc-2 (both technically humbuckers, but single coils in shape/size) in the neck and the bridge with a lace hot gold in the middle position. I thought I might be able to just go ahead and put a humbucker covers on top of the Chopper and Bc-2.

Will this extra layer of material muffle, or compromise the sound of the pickups?
There's a tiny, tiny difference. Some people care, I'd bet that most do not, or not enough to value the tone shift over the visual appeal. I'd call it more of a different tone than a muffled or compromised tone. If it were really noticeably worse than no covers, nobody would use them.

Raising or lowering the pickups a little bit will give you a similar change, so you can do that to sort of gauge the difference you might get.
Covers can only effect the sound if they're made of particular materials. These days it's actually harder to find a cover that will effect your sound than one that won't; it's something you really have to go out of your way to hunt down.

Basically, brass covers will reduce the highest frequencies a little, similar to taking your tone control and moving it from 10 to 9. It's a tiny, tiny difference. Even so, brass covers are very rare. Reproductions of original Telecaster neck pickups are pretty much the only place you will find brass covers being used.

German silver/nickel covers are the standard, even on cheap pickups. These categorically can not effect your sound unless you do not wax pot them, which can lead to very slight microphonic qualities in some rare cases (though this can happen with any cover that is not potted, even plastic ones).

The main reason why people often feel the sound has changed once they have removed or added a cover is because they have not put the pickup back at the same height it was before. The height of your pickups can drastically alter the response you get.
Yes, I know everything. No, I can't play worth a damn.
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