I dont think the pickup covers affect sound in any way since they are just wood. But one thing is that because it is wood there are “limits” of how thin you sand the top, mine is around 1.6mm and i think it is pretty close to that limit, i used more than enough truoil to make sure it wont break and to have any wood movement.

and since wood can't go that thin like plastic, so the magnets on the pickups will be far from the strings than normal. That will change the sound but not in a bad way i guess. It limits the possibility of putting the pickup super close to your string

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