Holy shit I never thought about doing that best idea ever to clean up any scuffs or pits.You can fill any gaps with silicone or glue/sawdust mixture.
i am guessing it wasnt MDF that you stained though was it? i also thought some dense wood like pine or soemthing stained looks clean too.iv liked staining the boxes i did that with the last box i bult and it looked really nice in the trunk.