All this worry about "arguing with the AHJ!"
The opposition seems based upon a religious belief that flexible cords ought not be inside pipe, and that there can be no tolerance of such heresy.
No one seems to recognize that this whole issue is the direct result of the NEC making a 'design decision' to ban flexible cords from above dropped ceilings.
So, why did we ban cords penetrating drop ceilings? I seem to recall a few folks arguing at the time that the soft cardboard tiles would damage the cords. Then there was that whole fire/smoke issue.
So, what's a 'drop ceiling?' It's a framework filled with rather insubstantial tiles. By definition, there's quite a distance between the ceiling and any structure- if for no reason than that one must be able to remove the tiles.
Why is this relevant? Because boxes must be supported- and we've had recent code changes that preclude supporting anything from the grid, even though there are some very nice brackets marketed for that exact use.
Plus, a box anywhere near the tiles will interfere with the removal of the tiles.
So, what's someone to do? Well, it's no trick to have a length of pipe to be 'cantilevered' from it's last support. Let that pipe pierce a tile, and you have a nice, clean penetration. All that remains is the transition to the cord.
So, I'd look to 400.14 as providing me with a loophole big enough to drive a circus train through. To wit: "In industrial establishments where the conditions of maintenance and supervision ensure that only qualified persons service the installation, flexible cords and cables shall be permitted to be installed in aboveground raceways that are no longer than 50-ft. to protect the flexible cord or cable from physical damage."
Since the NEC does not define any of the qualifying conditions in that section, the AHJ has no choice but to grant the greatest possible lattitude to 'industrial,' 'qualified,' 'supervision,' 'ensure,' and 'protection.'
Therefore, the NEC specifically allows that you run the cable through a fitting into pipe, and to continue the cable to the junction box.
How far to the junction box? Well -apart from the 50-ft. limitation- the pipe is required to be supported within 5ft
(not a typo) of the structural support, I'd say that the junction box would be required at that support point.