I think I have a layer of dark blue under the (white) gelcoat on my 1976 E27. Does that sound right? It looks like a fender may have rubbed through the gelcoat exposing a dark blue layer.
It is most likely that the stripe down the side below the rub rail was done in gel coat from the factory. the would have masked off the stripe, sprayed in the white gel coat, removed the mask, then shot in the blue.
That is the norm. My boat has been painted above the waterline. I just removed about an 1/8" of bottom paint to get to the blisters and the gel coat to repair, barrier coat and anti foul. At the Waterline I can tell that the boot stripe and hull were both gel coat.
I have the same "blue" showing through a bit on my '73 E27 where the fenders have rubbed the white hull. My boat has the original gelcoat. I'm not a boat maker so I don't know what the blue is, but it indicates the outer white gelcoat has been rubbed away.