As long as the texture is mostly green you can still do the colour swap. Its only when the texture is white grey or black thet it becomes especialy difficult (grey is not a colour). It is still possible to do a colour swap on a grey colour it is more difficult, and why make life more difficult than it has to be, right?
When making a unit, you have to think a little about colour theory. Basicly on the colour wheel you have three primary colours; red, blue and green, And three secondary colours; Magenta, yellow and cyan. You should have a colur buffer between the civ colour (blue) and the main vehicle colour (often green) as this gives the best result where the civ colour does not become confused, or bleed in to the main colour.
So;
#1Green=main body
#2blue=civ colour
#3Magenta=transparency and shadow/smoke
#4cyan=not used
#5yellow=flames
#6red= Desaturated red can be used as pink, and desaturated yellow/red (orange) used as brown, these are good for skin tone and wood/natural fibers.