Actually, Kevin, the setup makes sense to me. Even though the cubes hold SDKs for the ball and toe rolls, I think it's ok to have the cube's transforms control the overall foot position and orientation. It's faster to rough out animation this way. Ball and toe rolls are extra details that can be handled with SDKs.
Nevermind me. I'm just whacked in the head.
FYI, I don't usually use SDKs in my foot rigs, so I was just curious why yours was setup the way it was. I tend to hand animate everything.