Over the years I'd seen a lot of them that color. Though never on later EB's, like was said.
I always "assumed" that it was used by Ford on special builds or otherwise haphazardly. Like HD cars, or limited-slips and such. Units like the Nodular iron "N" cases in the big engined Mustangs and the like.
Maybe Andrew and/or Todd know more, since they've been around factory race trucks and special edition Broncos and, in the case of Andrew at least, a lot of vintage Mustang stuff.
Not surprised to hear they were stock in EB's in the early years, but always wondered why some were painted and others not.
Regarding the rust and primer issue, I don't know that what was used from the factory was actually a "primer" so much as a top coat type paint. Not only were many of them without rust many years down the road (though some were definitely starting to rust), the finish looked to my eye to be smoother and more semi-gloss, than the usual "flat" primer.
Are all primers flat though? I'm not a paint expert by any means. I just feel like the color was more "satin" than flat.
Paul