Funneling all passengers through a grand entrance, concourse, fare gate, etc., all along the skinny axis of the building, while perhaps architecturally spectacular, does nothing for passenger throughput. Caltrain monthly pass holders need to get from the street to the platform, pronto, without any scenic detours. (my bold)

The only way they will get a workable box under these circumstances is to make an engineering firm the lead on the project, specifically charged with optimizing flow and human factors.  Even if they so charge a lead architect, they will find a way to do the visually spectacular thing, regardless of the impact even on financial viability.  They can't help themselves.  The lead engineer should hire a capable but small and relatively new firm to help them optimize appearance around the given optimal functional design chosen by the engineering firm.  If they make the architect lead, they are almost certainly doomed.  

"It is not necessary to have hope in order to persevere."