There appears to be a lot of confusion about the relation between PTv2 & the original railway/highway schema. Worryingly this confusion extends to those who conceived the PTv2 schema.
Even though they tag the same objects they are separate schemas.
They are not dependent on each other.
For example, tagging an object with railway=station does NOT mean that the public_transport=station has to be added. In fact, there are many railway stations that aren’t used for public transport.
Those are the reasons why I remove references to PTv2 tags from various key:railway=* webpages.
Key:railway page should not contain any public_transport tags.
Specifically about railway=stop they should be placed where the engine stops, but I don’t really care as it will never be used.