Who knows?

If you are lucky enough to have seen this stuff when it's all apart, say engines and transmissions in the back rooms of old yards, or stripping and scrapping cars on your own for years, you see different things.
If you're like me, you make a careful mental note of something that seems unusual and remember it when you see it again and again, then you realize something that seemed odd is the norm, you just might not have seen a paint mark before because time and harsh salt may have rusted it away, or someone re-painted it 2 years after the car was built.

Mind you, I haven't memorized paint daub colors on transmissions, but I do know that an orange splotch on an 8-3/4 chunk means it was originally built with a suregrip.
I do know that every manual trans built did have at least the last 2 or 3 digits of the part number stenciled in with varying colors of paint.

I have been around extremely low miles original manual trannies and those were sometimes semi-gloss (chassis) black.
They were also painted a brown color resembling primer, as were some '489 case center chunks.

Mark.