Firstly from the pics i have seen, yours is not channeled. Channeled is when the body has channeld sections made up into the floor so it can sit down over a seperate chassis.
Yours looks to have had the rails moved inwards. This is called narrowed rails and is done when full tubs are to be fitted.
Most minitrucks get their rails notched vertically so that they can sit down over the diff without hitting on the diff.
NSW RTA guidelines only rule out narrowing of the chassis. This allowing the minitrucks to legally be notched if engineer approved.
With your ute looking to have used the stock rails. If you fit a standard looking floor, it will continue to look stock. If your rails are moved inwards to the extreme. Upon inspection it will likely be picked. But keeping it within reason and fitting average width rims for inspection will keep it looking like its only mini tubbed and this does not require inspection.
Quite simply no nsw engineer will approve it unless you go IVC like you have been told.