'Twas the exigencies of early color TV. The TOS cast wore primary colors: red, blue, yellow (okay, a sort of yellow-green that's termed "heather"). Nothing to get hung up upon, and for all we know most non-human crew were color blind, or read both "red" uniforms in different ways. For example, maybe engineering red looked very different from security red in ultra-violet.
Human eyes are not the only eyes in Starfleet.
No, but we can safely assume any eyes that can see higher frequency colors are much smaller and any eyes that can see lower frequency colors are much larger.