Lots of systems were initially designed with suboptimal/superseded technology, and over time, adjustments got made. In Spain, for example, they simply abandoned the old gauge and went with standard gauge when building new high speed lines so they could connect outside the country. The problem with BART is its governance structure: an independent government agency that competes with other transit agencies in the same geographical space, and has no particular incentive to serve the greatest need.
An example is in san bruno, where the BART tracks go directly underneath the Caltrain station. San Bruno is the last BART stop between SF and the SF Airport, so it would be a perfect place for a connection between the two systems. But BART chose to build its San Bruno station over a mile away, to serve the Tanforan Mall, and to forego a connection with Caltrain there. I think the reason is BART realized if you could get off BART at San Bruno from SFO, you could take an express train to downtown SF, and BART would lose business (although it would be great for passengers, of course). So the result was the terrible triangle of BART's San Bruno, SFO, and Millbrae stations. Instead of giving both SFO and Millbrae bound train passengers the option to change at San Bruno, which would have served riders much better, they built it as an either/or, so that Caltrain-bound BART passengers had to take a Millbrae train. After a few months, they "realized" that the connector between Millbrae and SFO was not economically viable, so they started forcing transfers from Millbrae Caltrain and buses to take BART to San Bruno and then change trains to backtrack to SFO, for most of the day. Before the BART extension, going from Millbrae station to SFO used to be a free, quick, and reliable shuttle ride. They turned it into such a time-wasting mess that it is a disincentive to ride Caltrain. But of course that suits BART just fine, because they can't make money dedicating trains to shuttling passengers from Millbrae to SFO, but they can make money by being a monopoly provider of train access between SFO and SF. If the two systems were governed by a single agency, I think they would make rational decisions like connecting BART and Millbrae at San Bruno.
It is BART's priorities, not just its tracks, that are misaligned with other systems.