i'm up in sac regularly, you should have no worries walking from the station to the hostel at 9pm
for more fun you could take the F-market historic streetcar from fisherman's wharf to embarcadero and then just take BART to richmond and get on the CC there
it's probably still worth the upgrade just because there's less of a chance of sitting next to a crying baby at 3am. but it's pretty much just a normal superliner coach car with slightly nicer seats. it's not 2x1 seating.
of course the warnings about oakland from outsiders are a tad ridiculous. you're not going to get shot at in jack london square, especially near the jack london inn. if you really need to not go to oakland there are two hotels in emeryville within walking distance from the station, one is...