Uh... the cargo cover is designed to come off by removing the "silver" bolt on each side... The brackets, hinges, and gas struts stay on the cargo cover so that every thing stays in alignment.
To put the carpet in, the "attached to the truck" half of the bracket must also be removed, as you describe. But this is ONLY when doing the carpet/bedliner, wiring work... and, yes, I've done the carpet kit.
So anyway, back to the cargo cover, for your future reference and for anyone else reading this thread and seeing the photos: DO NOT remove the six bolts to do a "normal, every day" removal of the cargo cover.
SEE PAGE 2-36 OF YOUR OWNERS MANUAL, it describes how to remove and re-install the cargo cover with only the silver bolts... and this is the first step of doing a bedliner carpet kit. Just remove the cover normally.
And, welcome to the carpet club! Ain't it cool? And, I love your painted accessories... very slick.