My truck is a Task Force era, 2 ton. The factory lines were all inside the frame rails. From the MC to the Hydrovac, then to a tee mounted near the Hydrovac inside the frame, then to the rear and front along the drivers side frame, then another tee at the left front wheel inside the frame, from there it crosses under the front cross member to the right front. I would think going under the frame rail would be fine as long as it's protected by the axle or other suspension component. Make sure the lines are secure so they don't vibrate and rub.

1957 Chevrolet 5700 LCF 283 SM420 2 speed rear, 1955 IH 300U T/A, 1978 Corvette 350 auto, 1978 Yamaha DT175, 1999 Harley Davidson Softail Fat Boy