A reply from my boss to one of the electricians in our area...
"725.48(B): "Class I circuits and power-supply circuits shall be permitted to occupy the same cable, enclosure, or raceway only where the equipment powered is functionally associated" In the case of these installations the 'equipment powered' is normally the dwelling or building. Class 1 circuits are installed under a different set of requirements than other circuits so it is very important that they be kept separate from those other circuits unless those circuits are indeed functionally associated with the class 1 circuit. We do not see how the building and its various equipment is functionally associated with the start up process of a generator which is NOT powered by those circuits; nor do these class 1 circuits have any control of or affect on those circuits being powered.
The signaling circuit shall not be in the same raceway with the power conductors
The whips shall have the proper UL marking on them or the installation shall comply with Art 725.48(B)
Also,
According to the U.L. white book: "Prefabricated wiring assemblies are marked with the conduit, tubing, or cable type, and the conductor size and type to permit determination of their suitability for a specific application and ampacity in accordance with the NEC. A parts list is provided with each assembly to identify the extent of the product". These markings are NOT being provided. Consequently we can not even accept those whips that come with the transfer switches unless they are marked by UL as being suitable for the particular installation."
If the manufacturer does indeed state this, as a CYA, or for any other reason then yes I agree 110.3(B) does not permit the wiring methods to be put together.
Also as stated on another thread a couple years ago on this topic, the term "functionally associated" as used in 725,48 is a very ambiguous term. We interpret that to be like the start up and run circuits in a motor circuit. Not the start up of the generator and the feeder circuit to the transfer switch.... Again that is our interpretation. So we still have 110.2 which ultimately is left up to 90.4
FYI in our state and more in particular our jurisdiction, it is illegal for the DIYers to install any electrical work. Much less a complicated system like a generator back up system with an automatic transfer switch.... Face it, if we as the "qualified persons" can't always agree on these issues, how can the DIYer even start to understand them...