There was an article in 3d worls about how ILM made them.
Basically they made the robot then fudged it when it transformed so that the geo went overitself in some cases to fit the robot into the car etc etc.
IF it was me I would model the thing you want it to transform into, then take the geo and pose it so it makes the robot then go form there.
"No pressure, no diamonds" Thomas Carlyle