San Jose, Oakland and Emeryville are all relatively long stops on the Starlight. San Jose is an engineer change with a scheduled 12 minute dwell and is always a fresh air stop, but never a smoke stop as smoking is absolutely forbidden on San Jose station property.
They tend to really discourage people getting off for fresh air/smoke breaks in Emeryville because of the number of passengers getting on and off there, though they are scheduled there for a 10 minute dwell. Oakland is scheduled for a 15 minute dwell, and they are usually ok with people getting off there, but usually make an announcement discouraging people from going into the station.