POSSIBLE FIX!
As someone in another thread mentioned, the look of a double linebreak is one of the big things stopping me from just search-and-replacing the entire multi-million word document.
BUT
A bit of googling revealed to me that putting a double-space at the end of a line is all MultiMarkdown needs to consider it a new line! So I did a search and replace, swapping “new line” with " new line", and it worked!! Now I just need to do that before each export, as well as doing a search and replace on my entire document.
Posting in case it saves anyone else’s bacon as well.