I'm not sure I fully follow the routing but had this been required emergency power rather than the optional standby power for a call center would using the same trough for the supply and emergency conductors violate the code? Would allowing the normal supply conductors to enter the disconnect before being routed to the transfer switch be a problem?
I'm thinking here of the language in 700.9.
700.9 Wiring, Emergency System.
(B) Wiring. Wiring of two or more emergency circuits supplied from the same source shall be permitted in the same raceway, cable, box, or cabinet. Wiring from an emergency source or emergency source distribution overcurrent protection to emergency loads shall be kept entirely independent of all other wiring and equipment, unless otherwise permitted in (1) through (4):
(1) Wiring from the normal power source located in transfer equipment enclosures
(2) Wiring supplied from two sources in exit or emergency luminaires (lighting fixtures)
(3) Wiring from two sources in a common junction box, attached to exit or emergency luminaires (lighting fixtures)
(4) Wiring within a common junction box attached to unit equipment, containing only the branch circuit supplying the unit equipment and the emergency circuit supplied by the unit equipment.
Any help in understanding the application of this article using the above physical facts as the example would be appreciated.