i'm also doing the research (mainly for a rack to carry bikes, etc) and there's a couple options
Pace Edwars Jackrabbit (retractable cover) with explorer rails
Pace Edwards Ultragroove, rails are built in (retractable cover)
Truck Covers USA American Rack Systems, rails compatible w/ yakima and thule extra, also retractable cover
Undercover Ridgelander with rails built in, and a rail system when you remove cover (1 pc hard cover)
Alternatives are a cover that doesn't cover the stake holes (such as Peragon, potentially) and either
Putco bars and rails meant for stock car rails, or
A stake pocket rack, such as
https://www.usrack.com/responsive/galleon-truck-rack.php
or something home-made such as stake pocket mounts, some bar tubing, and a rack kit meant for permanent mounting, such as
this image