So, coming back around to the whole miniskirt debate, I reconnected with Andrea Weaver, who was the women's wardrobe person on TOS for the 2nd and 3rd seasons. She literally put (sometimes sewed) the women into their costumes, so she handled them daily.
She said that under the skirts they used "standard dancer briefs" [dyed to match the uniform], and that the the idea of some sort of leg panel or such is "completely unauthentic". We've seen our share up upskirt shots on the show and this seems to jibe with her description.
When asked about the uniform colors, she said the idea was to use primary colors: red, blue and green instead of yellow. The green was green (not gold or lime -nothing with yellow added). She explains that blue is a very unstable color—"especially in L.A." (presumably referring to the garment district)—and when you see uniforms decades on they have lost their blue AND faded, so you don't see the original color. You can see this in the blue uniforms as well, many of which have color-shifted towards a pale purple.
So there you go. From about as primary a source as you can get.