Triple:
In most cases, the 'large' air handlers are 'factory assembled' units with NRTL listing/labeling, etc.
The sealing at penetrations should be done. I can't give you an Article at the moment. Sealing may also be required within the mfg install directions, or job specs.
Determining if the 'walk-in' areas are considered plenums, or are considered a 'regular area'. IMHO, whatever wiring methods that are 'factory' should be acceptable in the same area.
As to the enclosed (plastic) fluorescent fixtures, depends on the 'plenum' or regular area decision. Most I have seen have 'jelly jars'...
