(Maybe you've already considered this, but...) You could also transfer from CZ to SJ at Martinez - save a few miles and bucks, and overnight in a more pleasant, laid-back small town, where Joe DiMaggio was born and John Muir chose to live (I'm old enough to recall the former, but not the latter). I made the SJ to CZ transfer here just last year, spending the night (and less than $100.) in the altogether decent Muir Lodge Motel. Alternatively, you could save even more time/money by detraining in Sacramento, where there is a well-regarded Vagabond Inn and a number of things to do near the station, and connect with the SJ by bus in Stockton the next morning.
But unless you plan to take the bus over to San Francisco, there's little in Emeryville itself to warrant an overnight stay. It's an industrial/commercial area with several large, expensive hotels, but no restaurants, or places you'd want to be walking around.
