Several things are taken into account for engine exhausts.

Color is calculated by combining diffuse and glow in spg2_thruster.fx shader (editable with Notepad).
Output.color2=color*color.a*siMapMult; //Glow
Output.color = color*diffuseColor.a; //Diffuse

Glow intensity
SIMapMult material parameter is used to change glow intensity.
0 = no glow | 1 = 100% glow (can go higher than 1).

Model transparency
DiffuseColor: alpha material parameter changes the models opacity.

Alpha channel in the model's texture ONLY affects glow transparency.