I've never seen a BART station shorter than ten cars, though many rush hour trains only use eight or nine.

I seem to remember that BART has an outdated and overwhelmed computer system which requires greater spacing between trains (and sometimes fails all the way down to manual control). At least new cars will have three doors instead of two, which should get a train out of a station faster.

I think I've been on trains in Japan (albeit not in Tokyo) where the first two cars didn't fit on the platform, and passengers were alerted to switch cars if getting off at that station.

Not sure how well it'd work given commuter congestion, but it warrants some consideration.

When I lived in Barcelona there were some low-traffic platforms shorter than the trains that went through them. I think the cars at the end of the train had big warning signs that they wouldn't open at station [X].