Overall, what is trying to be done is allowing for players to have a higher degree of customization on their ships.
The other approach would be if the squadron code could be modified so that it wasn't limited to 4 vertices. Instead custom geometry and UV map could be applied to the .pof file which would be recognized as the "squadron logo."
The idea behind this would be that then elements such as the logo, stripes, pilot name, face, etc. could be easily edited and selected as part of the 'squadron logo' without editing the main texture in this case.
For the pilot screen, a section of the UV map could then be selected as the part shown there.