I'd support moving eBART into BART and reducing by a system (though I'm also open to keeping it separate as its a somewhat different thing*). But the Oakland shuttle doesn't remove a system, and means it's missing from the other similar routes.
Plus the shuttle is not given a colour. If it was 'grey line' or something, then that's treated as equal. It's not even given a letter.
*But, where these transfers to non-electric trains happens on Metro North and the LIRR, we've treated it as one route, rather than a separate bit.