You need to remove it, and the installation instructions for the rail system even state to remove them. - I attempted to keep them, however the track does sit correctly, nor are the bolts long enough.
I stand corrected, @MavStangVa is right. Upon investigation I see that Ford uses that whole indented area for the rails and does not install the forward cargo hooks. Now, some after market or DIY solutions may shorten the rail to retain that hook YMMV. Mine has obviously not been used, being tucked up under my tonneau cover. The rear hook I've used many times to keep things from sliding around is not affected by the cargo rails. I have yet to really use my cargo rails using mostly the rear most part of the bed unless more is needed.