i recently had my entire rear sliding window unit replaced under factory warranty. my question is.... should their be any type of protective caps (or weatherstrip) covering the nut/bolt assembly? or are the end of the bolts supposed to come in direct contact with the back of the seat backs?
this is a supercab model .

 

There is nothing over the studs that hold the window in. I suppose if you wanted to put something over them you could use small vacuum caps.