Costume designer Robert Fletcher made up a series of color samples with the maroon color being chosen because director Nick Meyer liked how it stood out against the background of the bridge set. I've never heard of them specifically considering the TOS colors, but it had to at least cross their minds.
They were also limited by what colors they could dye the TMP jumpsuits since they needed to save money and reuse TMP pieces as much as possible. The maroon color worked well so TMP jumpsuits were dyed and modified to become the WOK crewman uniforms.
As for the flap on the maroons, Meyer wanted a swashbuckling feel to the uniforms and used moves like "Horatio Hornblower" and "The Prisoner of Zenda" as style references.
The flap was simply a functional bit of the uniform that the actors sometimes used. Usually they were only opened when something happened – life support goes out and the bridge gets hot, for instance. The flap interior color also designated rank levels– white for command level and tan for everything else. The flaps were always functional, even in background pieces. I showed the center uniform with an open flap to show command – it's Spock's from ST4. The other – Rand's – has a tan interior.
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