I haven't checked to see if this is it, but you might try GC3AppearanceDefs.XML in C:/Program Files (x86)/Steam/SteamApps/common/Galactic Civilizations III/data/Core/, as that file has <EngineColor></EngineColor> blocks for each preset color set, with lines in the block for RGB + alpha.

Pur did it do it ???

C:/Program Files (x86)/Steam/SteamApps/common/Galactic Civilizations III/data/ParticleScriptDefs/ has two files (EngineThrustingParticleEffect.XML and EngineIdleParticleEffect.XML) that look like they might have something to do with engine trails, but I have no idea how it'd determine trail colors by faction; there only seems to be a single color entry for each emitter listed, and the files don't define separate emitters for each faction.

C:\Program Files (x86)\Steam\SteamApps\common\Galactic Civilizations III\Gfx\Shaders has the promisingly-named Trail4.FXO.

C:/Program Files (x86)/Steam/SteamApps/common/Galactic Civilizations III/data/Core/ has GalCiv3GraphicsDefs.XML, which defines some things related to engine trails, but doesn't appear to directly govern the color of the exhaust trail.

There are also a number of *.objgfxcfg files, which I assume to be object graphic configuration files and so might presumably define something about the engine trail colors, if you can figure out how to open them. At least some of the drive components (hyperdrive, stellar folding, hyperwarp) and thruster components appear to be among these; possibly the trail colors are defined by something in one or more of these.

In the Core Folder you need to edit AppearanceDefs

Engine color:

<LightGradientRow3>2</LightGradientRow3>

Engine Trails:

<EngineColor>
<Red>255</Red>
<Green>178</Green>
<Blue>84</Blue>
<Alpha>254</Alpha>
</EngineColor>

The appearance internal name:

<InternalName>EVN_AOFT_Appearance</InternalName>

 Is referenced in the FactionDefs xml

<Appearance>EVN_AOFT_Appearance</Appearance>

You can find more info at the following links although there are a few others I cant remember:

https://forums.galciv3.com/466774/page/1/

https://forums.galciv3.com/461766/page/3/#replies

The following is a small text document I have open when I'm working on the appearancedefs xml nearly all of this came from Gauntlet and a few others in the links above although I believe I'm missing one:

***Appearance Defs Guide***

SurfaceScale1:
The smaller the number the larger the material texture is on these
areas of the ship, say surface material 3, which is the hexagonal
pattern, the larger this number gets the smaller those hexagons on the
ship become.

SurfaceWeight1:
This controls how much the surface material shows through the colour.
SurfaceScale2 & SurfaceWeight2: Refer to above.

***Diffuse Colors Guide***

DiffuseGradientRow1 = Base color gradient of ships

DiffuseGradientRow2 = Trim color gradient of ships

247 = Turquoise Pale
245 = Tan/Orange
33 = Black?
32 = White
31 = Purple
30 = Soft/Solid Green
29 = Dark Purple
28 = Light Purple
27 = Greenish Tan
26 = Pale Aqua
25 = Gold
24 = Weird metal green
23 = Even lighter Sienna?
22 = Yellow Sienna
21 = Pale Steel
20 = Sienna
19 = Blood Red
18 = Black?
17 = Dark Sienna
16 = Black with a hint of blue
15 = Black
14 = Dark Grey?
13 = Purply Blue
12 = Pale Light Blue4
11 = Krynn Orange
10 = Pale Teal/Green
9 = Pale Purple
8 = Light Steel
7 = Red
6 = Yellow Green
5 = Iridium Brown
4 = Steel
3 = Blue
2 = Aqua
1 = Blue
0 = Light Metal

***Light Gradient Guide***

LightGradientRow1 = Base color gradient for ship lights/lighting effects

LightGradientRow2 = Base color gradient of ship windows(cockpit)

LightGradientRow3 = Gradient for ship engines

254 = Alternates through all colors
253 = Very Glowy Yellow
252 = Yellow/White
251 = Yellow
250 = Glowy Red
249 = Light Blue Glow
248 = Bright Purple
26 = White
25 = Liht Blue
16 = Purple
15 = Blue
14 = Solid Yellow
13 = Green
12 = white with hint of yellow
11 = White with hint of blue
10 = Whitish Blue
9 = Light Yellow
8 = Good Yellow/Orange
7 = Light Purple
6 = Light Green
5 = Pure Yellow
4 = White Light
3 = Bright Blue Light
2 = Orange
1 = Light Blue
0 = Plain white

Hope this helps