Are you leaving the inner fenders in the car and just removing the areas where the inner doesn't touch, or are the inner going bye-bye ?? Either way, I would think the triangulation of a cage is far more superior than the little bit those pinch welds could ever give.
If you look at the rails as just a boxed tube, the reason for the seams are evident. They (Mopar) needed access to the inside of the rails for blind nut attachment, i.e. k-frame and bumper bolt mounting. It was/is a LOT easier to stamp a complex shaped piece then box it up, than it would be to start with a boxed tube. the flanges are nothing more than a quick way to mate the two pieces by spot welding rather than mig. and they provided a convienient attachment point for the inners.
Cut 'em off, weld 'em up, smooth 'em out and have a happy.
Todd