Being a first mover didn't prevent them from adopting standard gauge which already had existed for 100 years.
I don't think the gauge is a major problem. Train orders are always a custom project, few urban networks use exactly the same standards. Railroad manufacturers are used to different gauges.
In that case blocking the road and dropping in a new road bridge was affordable given the economic value but generally you put up with what you've got.
In practice I am not convinced the BART is severely impacted by their "weird" gauge (whatever is meant by that, not sure what their loading gauge is, for passenger trains the distance to and height of the platforms would be most relevant).
Stadler KISS series used by Caltrain is built at least in 3 different widths.
Auckland, NZ had (not sure whether still in use) rolling stock from the UK, converted from 1435 mm to 1067 mm track gauge, the loading gauge obviously was close enough.
Finland has engines (Sr3, Dr20) and railcars (Dm12) designed for smaller central European loading gauges. They look a bit tiny compared to other stock, but they are fully usable.