We've argued about this before in our office. I don't believe the building code is very clear (someone correct me if I'm wrong)... I believe the intent of the code is to design the connection of the superstructure to the foundation using omega level forces, but it doesn't explicity say to apply omega to the foundation design. That said, we've been asked by OSHPD "What's the point of designing to forces to be transfered to the foundation if the foundations can't take it?" Makes sense I guess. I'd design for omega forces, and no one can question you as being unconservative. Although depending on the building, it may lend itself to some pretty large foundations.