You could always separate the rear carpet section and put down some bedliner. You could even paint over it in a color that comes close to matching the rest of your carpet...
As far as that storage container, if you're looking for something bag-like you could try a local military surplus. You'd be able to see the size of the bag before you buy. Most surplus stores carry new items as well not specifically made for military use. The one here has some range bags that compare to the bag you posted.
The Quadratec covers the whole back floor with or with out the seat in. Picked one up last week...the matt has a space to pull the seat belts through... fits side to side and front to rear nicely. You will need rear floor matts for the foot space...
I think its a decent product.
01 Wrangler Sport 4.0L spd, 2" lift with 31's.
ARB Bumper with M8000 Warn and KC lights.
02 Kawasaki KLR 650
07 KTM EXC450
09 BMW F800GS