Not all rapid transit systems fall into the PATH situation, where they're subject to FRA. CTA in Chicago (and a lot of others) is not subject to FRA rules and regulations. Certainly in terms of rulebooks, crew responsibilities and the like they behave very much in the classic railroad sense, but with the recognition that they have much more frequent operations. Going to one-person operation has obviously changed their rules and operating procedures.
Until 1973, CTA ran interchange freight service from a yard served by the Milwaukee Road on Chicago's northside to serve a coal yard (and before that some other customers) along what are today the Red and Purple Lines. Gauntlet track was used to provide sufficient clearance for the mainline railroad cars with respect to the third rail. The 50-ton steeplecabs used to run the freight had pans and were powered off the catenary above the gauntlet track. By day the "normal" track (closer to the third rail) was used by CTA rapid transit trains, but there was no sharing of this track when the frieght was out on the line.
Hope this helps!