I use the RRS foot, for the reasons described in this post
. I honestly have no idea if the lens will fit in the Canon case with the RRS foot attached - I don't use the Canon case at all.
For carrying the lens to the field, I use the Lowepro Lens Trekker 600 AW II discussed above. It holds the lens with a 2x TC and 1D X mounted, has a tripod holder for my RRS TVC-33, and Sliplock attachments for lens cases, the Lowepro Lens Exchange 200 AW in which I carry my RRS PG-02 LLR gimbal head, etc. FWIW, the Lowepro Flipside 500 AW will hold the 600 II (no body attached), and it is
airline carrying size.
For storage at home, I want something waterproof - the Canon case is not. Roofs leak, pipes burst, etc. I keep my 600 II (with the hood reversed and foot on) in a Storm im2720 hard case, along with other gear:
I did use Loctite on the threads of the 4 screws when I replaced the Canon foot with the RRS foot (the Blue 242 type, so I can remove them if needed).