Another useful article by Aleh Cherp over at Academic workflows on Mac.

When I am doing academic writing bound for print, it always ends up finally in Word. Much like a final resting place. I wish it was not the case, but it currently has to be. In most academic work that I write there are numerous figures and tables that all have to be in the right place at the right time. While you can try to piece together captions and cross-references through many youtube videos, he puts it all in one place, in a clear guide.

His final point:

Transferring texts from Scrivener and then adding automatic captions and cross-references is certainly tedious so I am always open to an alternative solution for caption management.

While I do not have an alternative solution to this, a simple hack I use is a placeholder in my captions and text. The placeholder I use is "Table X" or "Figure Y". When the final text is placed in Word, I can do a simple find and update those with the proper caption or cross reference. While it still requires a good deal of manual work, they are at least easier to find.

Markdown certainly does not have this and I do not know of it in MultiMarkdown, but captions and cross-reference for the most part are things of paper and not the internet.