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The bed kit I got is different than yours. Mine is almost flush with the rear cross member. Yours appears to extend all the way to the end of the flange. I don't think your tailgate will fit like that.
I did have to cut the tailgate itself where the hinges fit. It was too wide so I cut it to fit.
The simple answer is that the flange should be as long as the bed wood...the end of the flange should stop at the same point as the end of the board. Bed boards are 78 inches in length.
Having an issue with the tailgate now. One side closes perfect, the other side falls short of closing about 1/2". It feels like it's hitting on something. I've looked everywhere. I'll post pics when I get home. It feels like it's binding because the other side is already closed. I've measured diagonally and I'm pretty close to perfect. Just over 1/8" off. Kinda feels like my tailgate is twisted or something....