Have you checked with them regarding torsion free mounting?based on the CA length of a crew cab F350, the biggest flatbed Duramag installs is 9 feet long.
I think the main reason people on here avoid a long rear overhang is ground clearance. The bed on that F350 would typically be 8' long, so sticking that out another 4' (to get your 12' floor) would be a lot. You could always angle up the rear portion to help with ground clearance.
One advantage the F550 has over the F350 is a smaller turning radius (for the same wheelbase). The F350's main advantage is a stiff boxed frame.