At the end of August, Caltrain added additional trains to their daily service to suit rush hours. With this and the Rush Hour update to Train Sim World 2, I feel it only fits to upgrade the Peninsula Corridor route with rush hour features. New trains added are to run at peak hours (6-9 AM & 4-7 PM), 4 trains every half-hour, and hourly Baby Bullet trains. The new trains also bring an opportunity to update the route with rush hour features such as working destination boards, expanded variety in passenger models, and larger passenger density during peak hours. Source:
According to this thread, they're working in it at the moment so will hopefully already be covering some of your points.