I would say they just picked some colours they thought were cool, and used them for the shiny. If it was that shiny forms were always inverted colours, then some Pokemon would seem strange.
For example, the togekiss. To me, it just seems weird because togekiss is supposed to be a happy, celebration-y Pokemon (it is the Jubilee Pokemon). Making it black, orange and blue just makes it a little evil-looking. It does look cool, but doesn't really match with what togekiss is associated with: peace and joy. A golden colour seems to suit it more.
Some shinies look ugly to people, but maybe they thought it looked cool when they made it, or having weird shinies was funny to them. We don't have any sure way of knowing how they make it. Maybe they use some kinds of filters. Maybe they just pick colours at random. Sometimes they just make it a few shades darker or lighter, like Glaceon. We have no way of knowing.