I haven't seen it mentioned in any of these threads, but you can set colors (and they are saved) for each of the base VF-1 models, from the options screen.
this allows you to, for example, set the color of the default VF-1S to red, and have Hikaru's DYRL VF-1S. the unlockable specific character VFs are done this way. you can even try out new colors that don't match anybody, or set the colors to gray for more of a low-vis look.
on the CF style VF-1A, you can change the entire tan portion to any color.
the only ones you couldn't do would be Max and Miria's VF-1J (set the color on the VF-1J to red, and you get Hikaru's though), and Max's TV VF-1A.