ORIGINAL: composer99
It's not the colours that are the issue, it's the air/naval unit bitmaps (see Steve's post #27).
As Steve notes, changing colours of units is trivial: you change a value in a CSV file.
But the bitmap backgrounds, which are in the current colour schema, won't change.
The air and naval unit bitmaps are anti-aliased.
Technically what is done is that the edges of the plane's/ship's image are made fuzzy by mutating them to match the background color. If you zoom-in using a bitmap editor, these images look rather strange. But at a zoomed-out level, the images become crisper that they would appear without anti-aliasing.
Changing the background color requires recreating the bitmaps from their original image and anti-aliasing them against the new background color.
I played around with using non-anti-aliased images early-on in this project and they looked like garbage.