Triple ... I think maybe you expect too much of the NEC.
Not to worry - you have lots of company. The NEC is, at best, but one element of an extensive web of standards and regulations.
First, you can't expect the NEC to specifically address every possible product out there. Nor is 'fire protection' the primary focus of the NEC.
Perhaps there is a UL, FM, or ASHRAE standard that addresses air handlers more directly. If so, these will contain references to still more standards.
I'll give you credit for recognizing that there is a difference between 'good design' and everything else; many times there are things that are 'legal' yet also stupid.
FWIW ... talk to the guy who maintains the "Ansul" systems in commercial kitchens; he can hook you up with fittings that will seal around conduit as it passes into something like an air handler.
