I don't see why it should be a problem, except on chrome and highly polished aluminium. You can spray just about anything over regular shades of alclad, as long as its fully cured. Alclad actually make their own prismatic shades (in clear blue, red, yellow and smoke) that are designed to go straight over alclad. Just make sure the paint cures fully before you spray anything over it.
Abdiel - I've heard that masking over chrome or highly polished aluminium alclad is not a good idea. But I've no experience of it so I could be wrong.