I'm old enough to remember why we pulled the covers from humbuckers. In fact my first set of Bare Knuckles were covered with a set of original 63 Gibson covers from a 335. We took the covers off to get more punch from the pickups. I think this occurred for 2 reasons. One is that we opened up the slug coils, and the other was we lowered the screws to be flush with the screw coil and raised the pickups a couple of millimeters. Both of these together gave that boost. In BK's case, Tim compensates somewhat for the cover, which reduces the difference, but as Dave and gwEm both say, the covered pickups still sound a little sweeter.