It all depends on whether the property in question is a "Railroad" as defined by federal law or not. If the answer is yes, the property is regulated by the FRA; if it's no, the FRA doesn't regulate the property.
IIRC (which you can check by going to the FRA website), the legal definition depends mostly on whether the property in question is part of the national railroad system, not on the type of rolling stock.
For example, the H&M was and, because of history and inertia (not to mention politics), its successor PATH is regarded as a part of the national railroad system and thus a Railroad while the NYC subway has always (at least since the current laws have been in force) been outside the national system of railroads and thus not a Railroad as defined by federal law even though the two properties use essentially the same kind of rolling stock to provide essentially the same kind of service.
It should be noted that each property has at least one connection to another rail property, one that constitutes a Railroad. So long as the connection is used only for deliveries by a Railroad to the property in question, it should have no more effect on the status of the property than any industrial siding owned by any other Railroad customer. OTOH, start running regularly scheduled pax service over that connection and you've made a really good argument that each property is a Railroad.
SIR, BTW, is just more proof that once trackage is owned by a Railroad (the B&O), the Govt. is loath to admit that the trackage is no longer part of the national system, even years after the only connection to the rest of the system has been obliterated.