Very long stories can do this, especially when there are cross-references or hyperlinks, etc.
I know that Adobe is working on improving performance. (If you join their prerelease.adobe.com program, you can test out their newest beta and give them feedback on whether it’s working better.)

In the meantime, one option is to break the stories down into smaller threads:
https://indesignsecrets.com/how-to-split-long-story-into-smaller-pieces-unthreading-middle-story.php

You can probably just put one of these nested styles inside the paragraph style applied to the TOC paragraph, too, yes?

Difficult!
The first place I would look for a (partial) solution is in these scripts: https://www.kahrel.plus.com/indesign/footnotes.html

Hi Stephen: Thanks for sending the file. This is a great example of how a tiny feature can make a huge problem. :-)

The problem is that the paragraph style applied to your state subheads is set to span 2 columns! That created a “zone” so that the text couldn’t flow into it.

Sure… send it to David [at] indesignsecrets.com