Are they based on existing paint schemes or canonized afterwards? Or might these be a case of "No one has gotten around doing either one yet"?
Some choices certainly seem to be unusual for some factions, like MWDA Cappies using orange and dark gray/black.
No, they weren't any specific established paint schemes. The schemes used colors that would likely identify with that faction. There were 3 "Units" per faction based on skill level, and the colors were divided based on that unit. The low level unit was mostly 1 color, the mid was a split and the top end was mostly the other color. This was all mostly to make the units visually distinctive on the battlefield.
And it worked, I could tell which faction a piece belonged to from a distance, which isn't always the case with schemes from BT products. Take Clan Wolf, most schemes are various browns or grays, but Alpha Galaxy is green, the same as hated enemy the Jade Falcons. Then the Falcons are mostly greens, some yellows too, but Vau and Lambda Galaxies are grays with blood red, better for the Blood Spirits. The Spirits are mostly reds with assorted other colors, but Tau Provisional Galaxy is black with copper uppers and red accents.
I could go on and on pointing out examples of what we think are unusual and non-traditional colors for a faction, but I think most folks' eyes would glaze over and it'd take me a lot of time.