Maryland Area Regional Commuter Rail (MARC) recently changed its policy to allow bicycles on most Penn Line trains, joining all the other major commuter rail systems in permitting bikes on rail. Unfortunately, like many of those other rail lines, its policy is also limited to non-motorized bikes, meaning they exclude e-bikes.
It's gotten easier for cyclists to get around on MARC in the past year. The MTA announced in February 2019 that there are now bike racks available on 35 weekday trains for full-sized bicycles, available on a first-come, first-serve basis. Previously MARC only allowed foldup bikes on weekday trains. However, it still doesn't allow electric bicycles or scooters.
Of the 10 largest commuter rail systems in the US, only three—the Southeastern Pennsylvania Transportation Authority (SEPTA), the Massachusetts Bay Transportation Authority (MBTA), and Northern California's Caltrain—allow e-bikes onboard. Only MARC specifically excludes “battery-powered” bikes, while the others have a blanket ban on all motorized bikes.
Since most systems ban all motorized bicycles, it likely has more to do with creating a bright line to avoid allowing motorcycles onboard than it does safety—though there could be safety concerns as well. When asked to explain the reasoning for its policy banning battery-powered bicycles, an MDOT Maryland Transit Administration (MTA) spokesperson said only that, “MDOT MTA is currently assessing the safety of lithium battery-powered scooters and bicycles on MARC.”
E-bike battery fires do happen, but are extremely rare. They may be no more common than fires caused by other batteries like those found in laptops and phones, which are currently allowed on MARC and other commuter rail systems. Either way, I couldn't find much research at all on the risk of e-bikes on rail.
It's good that MTA is looking into the safety of allowing battery-powered mobility devices on trains, and it should err on the side of caution. However, it would be a shame if an abundance of caution limited the options for commuters looking for a way to get around without a car.