I got burned with that.
I was joyriding the Evanston Line to the end and decided to stay in the station to avoid paying another fare to get back in. The train left and stopped as you said. The conductor had this heavy belt with a series of fare registers (counters) for various fare types. I ended up paying a full fare anyway. If I had paid at Evanston that cashier would've given me a reciept for the conductor. Apparently the little stations in between are unmanned.
If I knew that operation I would've gotten off and checked out the ancient station and surroundings and got a few pics.
The Evanston Line is 3rd rail all the way but AFAIK the manual fare collection continues.
I've heard the Skokie Swift line will convert to all 3rd rail. That had an automated home-made pantograph conversion.
BTW, the NYC subway has a light line in Staten Island ("SIRT") where they did away with most fare collection. Most passengers are riding to the ferry terminal at St. George. At St. George one must pay a fare to leave or enter the SIRT line, but no fares are collected anywhere else on the line. So, if you are travelling between any station except St. George you ride free. Some psgrs get off one station early before St. George and walk about a mile to avoid the fare. Since fare collection was all manual, they saved two crewmen for each train who didn't have to swing through collecting cash or tickets.
At one time SIRT had a nice bucolic flavor to it but now it seems like any other subway, just with a lot less people. A recent station rebuilding replaced quaint wood shelters and platforms with heavy steel and concrete. More durable but not as attractive. SIRT was originally a branch of the B&O RR.