Hi Karen,
I certainly don't intend to defend either the Lomaxes or Lloyd's practices, although some of Lloyd's statements   quoted above are valid. On the detailed question of "the confusion in Infirmary where a woman dies but the funeral is requested for a man", this is only a problem in SJI itself, and not in the precursor song 'Gambler's Blues' - either the 1925 Moore / Baxter sheet music or the two versions in Sandburg.

Here its clear that it is the dead woman who’s being buried:

Sixteen coal-black horses
All hitched to a rubber-tired hack
Carried seven girls to the graveyard
And only six of 'em coming back

However, following this powerful Memento Mori, the narrator begins to think about his own funeral arrangements:
Oh when I die just bury me
In a box-black coat and hat... etc

So we don't really need to invoke the indeterminate gender of the victim in older versions to explain it.

Just because 'St James' Infirmary' was a hit record and is known to millions in a recorded version now set in stone, doesn't mean it isn't a garbled version of the tale, as so many orally collected folk songs are.