Think about the history of the humbucker and Seth Lover's Patent
the original thinking was not based on tone or power
it was noise cancelation. and humbuckers for years were based of this principle
there is usualy one dominet coil (screw polpeice) and one "dummy coil" (slug polpeice)
the cover further acted as a sheild and the screws protruted through this cover
to better pickup the vibration of the strings. but the dummy coil still colored the tone
(just like a capacitor) and a minor increase in power (biproduct)of the twin coils
enter the after market and the focus shifted to power(Super Distortion's) and others.
wich used both coils (no covers) to produce more power resulting in(higher mids)
now we are back full circle sort of (virtual vintage). one "active"coil one dummy coil
to obtain that single coil sound with no noise
so does a cover affect tone? that answer would be Yes
but most people would not notice it in a blind test
as far as PRS himself i read this in a guitar world interveiw for his 20th anniversery
to qoute Mark Quigley of PRS guitars
"on a hearing scale there are normal humans, then dogs, then Paul.
design and build for over twenty years and you too would be like him