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Then you need to support the train-specific OS, and find developers who know how to write code for this train-specific OS, and IT staff who can install the train-specific updates onto the train-specific OS.

As for why they would not use Linux? Leaving aside that these probably predate the wide adoption of Linux, Windows is often used in embedded devices which need graphical interfaces/displays. Again, ease of finding developers and third party tooling is a big driver.

There have been a number of things I've found running some old version of embedded windows that I've been suprised by

I don't get it either. Can someone familiar with trains explain what on a train needs a desktop OS? A train is more like a car than an ATM machine, I would expect a collection of computers running either bare-metal or an RTOS like QNX/VxWorks (the pictured train is from 2000, so embedded linux hadn't taken off yet).

You'd probably have an OS with GUI for non-essential services like lights, intercoms, A/C etc. And present some additional info in nice graphics: the state of carriages, situation ahead on the line (as a complement to just flashing a green/red light on the board). The rest would run RTOSes or similar.