Welcome to the FRF. I love my bedrug, but it is now over 2 years old and has taken some damage from racing jack getting loose and rubbed a hole in tailgate.
Here is an idea for a product for those who have or consider getting a cover, is an active fan system to create positive pressure inside the cargo area to keep trail dust out. I am not sure what causes dust to be sucked in under the F1 cover but if you perhaps mounted a fan right below the center window with opening facing the cab with filter would keep enough positive pressure to keep dust out.