As originally described in http://forums.autodesk.com/t5/ideastation-request-a-feature-or/define-rectangular-tubing-with-pipe-t... but then didn't get enough support.
Often working with non-square tubing and using sweeps for that gets a git tedious over time, started working on a script as a workaround but it's far from perfect: https://github.com/rambo/fusion360-Rectangular_pipe
It also adds a plane, a sketch, a sweep and a shell operation to the timeline instead of a single "pipe" operation so the timeline also get's very cluttered real fast.
On a side note: My script can handle multiple paths (unlike pipe tool), but there's another enhancement request about that already.