The employees' house magazine of the New York City Transit Authority published an article describing their telephone switchboard and system. They had twelve operators taking calls a PBX of 9,000 stations.
See: (click on item to enlarge)
It would appear from the pictures and text that the operators did not have a jack appearance for each station. Rather, the operators plugged into a series jack and dialed the number. For instance, to reach extension 2-4357, the operator would plug into the 24 jack row and dial the 357. The system probably had five digit extension numbers since 1, 8, 9, and 0 were typically reserved in PBX for special lines.
Many large transit systems had their own private systems for internal use which were not connected to the Bell System. The organization was large enough to have a staff to maintain the lines and switches themselves. I'm not sure if was the case for the NYCTA. While 9,000 stations seems like a great deal, the NYCTA was a very large organization. There were many emergency telephones located within the tunnels for use in case a train broke down. Likely on the bus division there were phones at major bus loops for drivers and supervisors to call in.