Set apart from the New York Subway system is the Staten Island Railway (SIR), which runs the length of Staten Island and connects to the Staten Island Ferry for the trip to Manhattan and beyond. While it operates somewhat-modified New York City subway equipment, it is part of the national railroad system, so the cars have meet FRA regulations and until 1997, fares were collected by on-board conductors. Since then, fare collection has been simplified and staffing reduced to a single operator.
Conductors make some sense on commuter rail systems: they have to raise and lower stair traps at stations with different platform levels and collect fares where trains pass through different zones. (Could zones be simplified on most US Commuter railroads? Yes, but that's the topic of a different post.) But the SIR runs subway-style equipment at all-high-level platforms with one fare, so all the conductor was there for was to to collect the same fare from everyone. And unlike most subway lines in New York, nearly everyone on the train was traveling to one station: the Saint George terminal and the connection to Manhattan. So when the MTA came out with the Metrocard, the conductors disappeared, turnstiles and MetroCard machines appeared at Saint George, and passengers paid a fare upon entry and exit (similar to the MBTA's exit fares when higher fares were charged for the Quincy extension). A few years later, after many passengers made the short walk to Tompkinsville, fare gates were added there, too.
But there was no need to put fare gates on the rest of the system. Most people use the line to access the ferry and get to Manhattan, and the cost of installing fare mechanisms at the other 20 stations on the line was far too high for the number of passengers using them, so travel between intermediate stops is free.
There aren't many other systems that could use such a procedure: most either have multiple fare zones or multiple terminal stations (shared with other services, making faregates less feasible), or both, making it much harder to implement these sorts of efficiencies. But in Boston, the Fairmount Line meets both these criteria, and would be a good candidate for this sort of fare system.
Now, before we get too far in to the weeds, let's posit that the Fairmount Line at some point gets more frequent service (the SIR runs every 15 minutes at rush hour and 30 minutes midday to match the ferry schedule, but the Fairmount Line should really run every 10 to 15 minutes), preferably from DMUs (or as this page has argued, EMUs). In the short term, four coaches and a diesel engine could be used for more frequent service, although doors might need to be automated. It wouldn't have the look and feel of a subway, but it could be operated as much as possible as one (frequent service, all door boarding).
Most Commuter Rail trains operate with three crew members: an engineer and two conductors; at rush hours, there may be additional conductors. Their direct responsibilities don't really extend beyond collecting fares and operating doors. These are important functions, especially for trains with 1000 passengers which run on lines which don't have full-length high platforms and with multiple fare zones. But the Fairmount Line has neither. Tripling the current headways to 15 minutes at rush hours and 20 minutes at other times could be attained with the current level of staffing (you need more trains, but not more staff, and the marginal cost of running a train is half staffing costs; likely lower with EMUs). That doesn't quite get you to subway levels of service, but it's a lot better than the hourly service today. There may be FRA issues with removing personnel from the trains, but the FRA does grant waivers, and the SIR operates under FRA rules with one person train operation. Other than a low-level platform at Readville, union issues and entrenched bureaucracy, what would keep the T from doing the same with the Fairmount Line?
Most everyone would pay their fare. The easternmost platform at South Station—tracks 12 and 13—could be set aside for Fairmount passengers with Charlie Card gates at the end of the platform, and a couple of ticket machines on the inside for passengers arriving without fare. Charlie Cards could (probably) be set up to allow a free transfer to and from the Red Line. If South Station is expanded, a Fairmount Terminal could be built with a direct transfer to the Red Line within fare control through the station's basement, although it's unlikely that the never-used underground loop could be repurposed for rail service, it could serve as a pedestrian passageway.
Since the first station on the line at Newmarket is a relatively-unpleasant, two-mile walk from South Station, there would be no Tompkinsville issue. According to 2012 counts, more than 99.5% of trips on the Fairmount Line were to and from South Station. With more stations open since then and possible free rides, a few more people might use the train for inter-Dorchester travel. Even then, the cost of collecting fares would still far exceed the fares collected, and any such travelers would not be able to access the rest of the system without paying an additional fare.
Unfortunately, the Fairmount Line is an ugly stepchild of the already rather ugly MBTA Commuter Rail system. Without increased service, it seems destined to serve few riders; while it provides relatively fast travel it is so infrequent riders are usually better off taking a bus and transferring to the subway. But with a relatively small investment in linking the electrification already present at both ends of the route, and with some common-sense fare payment initiatives aping the SIR, it could act much more like subway line straight in to the core of the city, with easy connections to other subway lines and the airport. And in a disadvantaged community with poor transit, this would go a long way towards better job access and prospects for workers there.