The only real upside I can find with the plan footprint is that 2 different dimension formats can be used. Decimal feet in the plan footprint CAD detail for complex site plans that need survey information, and fractional inches in the floor plan. When using floor plans Layer Sets Ref Sets etc. there is only one dimension format available.   Both methods have a 'live' footprint but Anno/Layer Sets seems much more flexible but can't access 2 dimension formats if needed.