The warp engine side windows (or more like top windows) of the Gagarin also glow red, don't they? That color, too, appears optional.
In "Yesterday's Enterprise", we were treated to our first example of non-red impulse engines (that is, if lit at all, and the "rampable" color of the TMP ship notwithstanding), and the blue there was probably intended to denote damage of some sort. ENT then decided blue is cool for impulse, which is sort of logical if blue means low power (although blue is of course a "hotter" color than red). But warp glow always remained blue, even when damage was shown.
Here we might continue to play the game that impulse colors relate to power levels. Heck, it was great fun to play with phaser colors relating to setting in TOS, before TOS-R uniformized the shots...
But we could also say that atypical colors are alien influence, that is, remnants of early diversity in the Federation, and that Starfleet standardizes on the TOS movie colors because it gradually abandons specific Andorian or Tellarite or Nevahurdian engineering practices and, after a century of trial and error, settles on an average or optimum of some sort. And the 2250s, with its 2220s-30s-40s-vintage ships, is not yet it.
Timo Saloniemi