Re: Covered vs Uncovered pickups
Agreed, there are way too many differences to simply say it's the covers. Heck, the pickups alone (especially if one is double-slug) is more responsible for the difference in tone than covers vs no covers.
HOWEVER, you might actually appreciate the change removing those covers would make. Tends to open up a pickup's sound slightly...a little brighter and clearer. It may not be night and day compared to the differences between those guitars, but removing the covers is an easy way to make a change you might enjoy. Plus, it's free.