The manifolds were painted with the engine colour at the same time the engine was.
The exhaust manifold burned the paint off almost immediately so your "flash rust" is the normal look for them. There are a few coatings guys have had (some) success with on the exhaust manifolds with various prepping and even with recoating religiously, but it's very tough to keep them rust free forever. Some of the POR products and high heat cast blast are a couple of the products that guys have had success with. Do lots and lots of reading on many sites and then prep them immaculately and you might have good luck.
