That's sort of what I thought, but the confusing part is the last chunk of the second paragraph.
Why can't my black chocobo benefit from my regular? What is the indicator on my screen to show me this explicitly? And on some boards, I've noticed a transfig spot and a mirage board slot. What's the difference there?
Ok so you're in the menu and you hit Mirage Boards and then pick a Mirage. You go to a screen with one-four mirages displayed inside these cubes that reflect their sizes. All of those boards are active at once. I think you can hit triangle on that cube screen to see the ability list? Anything that shows up on the ability list crosses between transfigs (except form-specific green abilities).
But then if you go to the Mirage Case and transig a Mirage, sometimes you'll have options that aren't on that cubes page. If you transfig to one of those and then check the Mirage Board screen, you'll see a different set of cubes and forms.