Your idea is great - go for it. I made a reversible baby quilt using the 3rd method that Minda listed in her links.
One side was blue and the other side was pink, but I didn't want to change the colors of the quilt when I bound it. So, I cut strips of binding from the blue and from the pink and sewed them together. Then bound the quilt matching colors to the sides. It came out fine.
If I were doing it with matching blocks of different colors, I think I would quilt it in a meandering design as many have suggested. Then if the blocks are not exactly the same size on both sides it wouldn't matter.
Good luck with your project. Show us pictures as you progress through the process. It will be an interesting adventure.
Connie