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.
dang, this is like the bibical contra's those nuns drove me batsh*t with in my youth GO RENO! ~S~