Fender used to paint everything sunburst by default, and if another finish was ordered, they just painted over the sunburst. They are not considered factory refins.
Fender sometimes did this but it wasn't by default (and not on teles as they were ash and blond as the standard finish) Fender custom colors (in the pre-CBS days) often did have the yellow dye that was used with the sunbursts (and the fullerplast) and typically had a white basecoat, the color coat and then clear. (candy apple red having an additional step - first the white, then silver - later gold - then transparent red then clear.) If they were in a hurry (or if a sunburst job got screwed up) they would sometimes finish a color over a sunburst but it was more of an exception - likewise, if in a hurry, they sometimes skipped the clearcoat (but not often).