I have a sort bed and used the above mat. I had to cut it down to fit and it worked great. I used the drop on my tailgate, covered all but 3-4". Saves my knees. It should fit your long bed well.
I just take it out and leave it in the garage when I need to use the bottom rails. If that's not an option, it easily rolls up. Just use a ratchet strap to keep it from unrolling. I also don't see where it would be too complicated to cut a few holes out where you need them in order to use the tie downs.
Don't know if you have dogs or not, but I feel the rubber mat makes the bed more comfortable for them because their claws and paws don't slide around and the bed surface gets leveled out providing them with a nice surface to lay down on.
I have a DeeZee bed mat that I use over my spray on liner and the utilatrack. When I need to use my floor utilatrack, as when I use it for mounting my custom bike rack, I pull the mat out. Otherwise I use the side utilatracks or the OEM rope hooks that I added to my P4X.