I only drop in on the forum once in a while these days; resurrecting this thread again with my take on covered vs uncovered.
Do covers make humbuckers darker or brighter? Yes.
Yes, they do.
I see it this way: even high quality covers can dim a tiny bit of treble, particularly the high airiness that we love about low winds.
So, all else being the same, pickups normally seem slightly brighter uncovered - though almost imperceptibly in many cases.
But here's the thing: usually all else is not exactly the same.
After a cover's installed, screw poles usually get raised to look level with the surface of the cover. Few leave them below, flush with the slugs.
Raising the whole row of screws even slightly can make for an audible change in some humbuckers; it affects the coil balance.
Adding a cover also results in both coils and magnet being a tiny bit farther from the strings when surface height is adjusted to the same spec.
Not much, sure, but with certain pickups a mere quarter turn on the mounting screws is enough to make a difference you can hear.
A millimeter can matter.
I think those factors occasionally make a bigger difference than any treble loss from the cover itself.
It varies from one wind to another, of course. Like many aspects of tone, not always predictable.
Still, It makes sense that sometimes a pickup will actually sound brighter after being covered, while others seem to become warmer instead.