I imagine that if we looked at some of the scout and other songbooks, we will find a lot more than red pyjamas in the song versions- and six pink elephants as I heard sung years ago. There should be a number of parodies.

I don't see any relationships to Mother Jones (1830-1930) in the older versions, although her lifespan covers the period in question. I would expect the verse to be more specific. If the song was being used as a reference to her, I would expect that Carl Sandburg or Lomax would have mentioned it. If someone wants to make up verses about her and her work for miners and others, however, why not? A good tune with simple meter always lends itself to changes and additions.

Vance Randolph collected these lines in MO:
She'll be comin' round the mountain, charmin' Betsy,
She'll be comin' round the mountain, Cora Lee, etc.
This in a song called "Charming Betsy," but it shows how song ideas move around. I have wondered if "She'll be comin'...." and "Charming Betsy" are related.