So I’ve been watching a bunch of lore videos and discussions about Fallout 4, and unsurprisingly for a poorly thought out game, the Railroad is a poorly thought out faction. There’s a reason people hurl the “SJW” moniker at them, made all the worse by their obsessing about their moral crusade to free the synths (a worthy cause to some extent) whilst the Commonwealth is a complete shit show, and caring about nothing else.
Yet I think there is a somewhat simple way in which they can be made into a more fleshed out, understandable faction: make them the former intelligence arm of the Minutemen.
It would explain why spying, passwords and isolated cells are their thing as spy craft was their primary job back in the heyday of the Minutemen. They’d have been the ones sniffing out raider attacks before they even happened.
In a very odd way, the Railroad would still behave as Minutemen even if the best days of that organisation are long behind it. Because in their eyes, Gen III synths are people, thus citizens of the Commonwealth. Therefore, when a synth needs them, the Railroad is there at a minute’s notice.
Edit: You can go further! Alongside freeing the synths, the Railroad could rightfully perceive the Institute as the primary threat to the Commonwealth and are trying to neutralise it.