Haven't seen this mentioned before, but CN appears to be lettering their ex-IC locos differently to distinguish them from their Canadian cousins. A freshly painted CN GP(?) in red and black, with black/white stripes came through on CSX between New Orleans and Mobile. The only difference that I saw was a big white "IC" on the cab directly below the windows. Sorry I don't have a photo, but when they're doing 50 mph and all I get is a slot between trees and buildings....you know how it is.
Hytec, They are lettering the IC units for Accounting reasons, same thing happened on Conrail Units when CSX and NS took over. CSX (NYC) NS (PRR)
Clayton- I'd say you have it correct. Remember how for many years Southern Railway (System) diesels carried subletters for subsidiary operations. I'd bet the same reason holds up. Boxcab E50