Noted, thanks. I started to make the new changes accordingly - sorry for the unintended consequences. I will fix those that we already changed. Just give me a few days.

If you can point me to wiki documentation indicating what the correct relationship should be between "train route" (relation), and "stop area" (relation), then we can hopefully get clarity. But the current documentation seems to suggest that there need not be a formal tie (I stand corrected, so please advise).
Best regards,
Johan

Noted, @azakh-world, Alexey. But they were tagged incorrectly to start off with. Stations should not be associated with the rail track (see railway=station ). Nodes on the `railway=rail` ways should be `stop_positions`, not stations. The `stop_position` is part of the train route, not the station (because a station means different things to different people). We need them to be `stop_positions` otherwise we cannot have navigable transit networks.

I am currently cleaning it up so we have navigable networks. I will add the stations to the `stop_area` going forward. When I'm done, I will go back and fix the others already changed.