They would not, the term you're looking for is "Loading Gauge"[1]. The US freight loading gauge is one of the larger ones.
That said there are other reasons a subway could end up being subject to Federal Railroad Administration[2] rules. I will note that I'm not an expert on those rules. But, generally passenger rail systems in the US are subject to Positive Train Control[3] or equivalent. It appears BART is actually one of the earliest adopters of Automatic Train Control[4], which appears to be a PTC equivalent. If not more automated.