The NEC cannot contemplate every installation that can be made in the field. If it could, we would have a document that could conceivably be a gazillion pages.
So, when codes are written, they try there best to cover as much territory as possible.
I am not sure how people say the conductors are not "pulled" through this wireway/auxillary gutter. Was the gutter designed and manufactured with the conductors in place?
So, even though this is a violation, there is plenty of room to install the conductors due to the layout of the gutter and equipment. This is another instance where the code cannot be forseen to not match the installation.
I believe that 90.4 (and I rarely use this section) would permit an inspector to say this installation meets the safety the NEC requires for installation. "...permit alternative methods where it is assured that equivalent objectives can be achieved by establishing and maintaining effective safety."
Now all we need is Special Permission. In NYS that would take a signature by the building official. It is rare that they give their signature for electrical inspectors work.