It's not just that - BART was simply never meant to be operating on the scale it does today. When BART was built, the creators envisioned a system that would serve about 100,000 people per week and choke points such as the Transbay Tube were built accordingly. Naturally, as the population increased, upgrades had to made. This worked for a while, but eventually lack of funding for serious overhauls caught up with the
constantly increasing ridership. Maximum capacity is heavily influenced by the fact that sections like the tube are single line, with no easy way to expand to double or triple. BART could theoretically be a 24/7 system, but as things stand now their engineers need every minute of the nightly downtime they have to service a rapidly aging rail system.
The rails already in place are almost at capacity, with a train crossing over them every 2 minutes. With the tech booms of the last decades, there's been an even bigger spike in these numbers. Over the last decade alone, passenger alightings at some stations have more than doubled. On busy days, the BART system now serves 25 times more riders than originally envisioned. There's some money for additional trains, but that can only do so much. Eventually, we are going to need to spend money on either more parallel tracks, cars, and bigger platforms or just a new system altogether.
Their administrators are simply being realistic about the situation we're in