Actually, 3d diagonal bishop moves work differently with the colors. Every 1-cube movement along a 3d diagonal changes color (1,1,1 to 2,2,2 for example), but that movement still only gives it access to half the board, despite having access to both colors. But yes, 2d "edge" diagonal moves stay on the same color regardless because they only occur in one horizontal or vertical plane at a time.
A 3d bishop could never get from 1,1,1 to 1,2,1.
2d bishop moves, any two of the coordinates change while one remains the same. In 3d bishop moves, all 3 of the coordinates change, but 2d bishops will never be able to access a cube where all 3 of the coordinates change in 1 move. Likewise 3d bishops can't access a cube where only 1 or 2 of the coordinates change in 1 move.
Best way to visualize the difference is a 2d bishop can move from (1,1,1) to (8,1,8), (1,8,8), or (8,8,1). But it could never move from (1,1,1) to (8,8,8) in any number of moves.
Your telling me that bishop should be able to change color is ridiculous. It's completely unnecessary, and I imagine you aren't actually visualizing what you are talking about, or you aren't stacking boards correctly. The example of putting a 2d classic chess board on it's side should show you that the pattern of colors on the board are a checkered pattern no matter what side you look at it from. Once you have that correct, you can see from simply looking at the 12 edges of the room you are in that the diagonal moves of the bishop follow the checkered pattern in all directions, all twelve directions. The bishop doesn't need to change color if the board is using the correct checker pattern across all three dimensions, as it should be for the board and the bishop. I'll say it again, you don't have a "real" 3D cube chess if you can't play it, you have a fantasy.
Nah I used all the same standard chess pieces, just more of them and both 2d and 3d moves combines for each.