@DavidGardner Could you clarify whether this is still the case for “normal” scripture, where it starts with an introduction in single column, and then switches to double column layout for the rest of the book. Surely in that case the footnotes from both the single and double columns would appear at the bottom of the page (as they have in the past).
I think the situation described above is a special/theoretical case where it goes from 1-col to 2-col and then BACK to 1-col all on the same page - in which case I would also expect it to do something strange [almost in retaliation for being so complicated!]