I don't know about SF and BART, but in NYC it's not just a matter of telling you to board the next train. Since there are multiple possible routes from A to B it may well be that needing to take the next train moves one route from optimal to suboptimal.

So yes, ideally the app would know that you can't walk a city block and two flights of steps in one minute and nix that as a transfer option. Bonus points if it told you which part of the train to get on to minimize the transfer time.