Yes, that is generally how Span works.
When you set a paragraph to span, you’re making a new “zone” inside the frame. It’s almost like a new frame inside the frame. So the zone above it (where the other text is) acts like its own little 2-column frame.

Well, first of all, that looks like a totally fascinating book. I love the concept of Interclusivity, which I had not heard of.
Anyway, as for the problem you’ve got… yeah, that’s a limitation of InDesign — a single row cannot break across pages. Some people fake it by splitting the row into two. Or they avoid it by setting up this kind of layout using something other than a table. (For example, you could have a heading, followed by a tab, followed by the description… and then make the heading “hang” with a large left indent and a negative first line indent.

What about setting the Vertical Alignment to “Bottom” instead of “Top” or “Justified”? That way, the bottom would always be in the same place (but the top would be different).

You can change the text frame in 12 point increments by setting your measurement system to Picas, then place the cursor in the H (height) field in the Control or Properties panel, and then Shift-click the up arrow on your keyboard. Shift-click will move in 1-pica increments, which is 12 points.

Dhafir’s code works great for me. This finds everything inside parentheses that has between 1 and 4 characters. Are you sure you’re using curly-braces? (?<=\().{1,3}(?=\))

Yes, as Steve pointed out, the in5 plug-in is excellent for exporting HTML.
Another option is to use File > Publish Online, which can export InDesign documents to the web.

However… It sounds like perhaps your issue is the TOC links?

I usually like to keep all my chapters in a single document, but this sounds huge… I wonder if splitting each chapter into its own INDD file would make more sense, and then managing them with the Book panel.

We’re going to have 2 days on the topic of “Long Documents” at CreativePro Week this year (Thursday and Friday sessions). That might be a good place to get some advice, too.

Barbara, are you saying you have objects moving up or down on the page? Or are they just shifting left and right?

It’s important to note that InDesign has a known feature (not a bug) where objects on master pages may appear to shift left or right when you add a single page in the middle of a facing-pages document — because the left-hand pages are turning into right-hand pages, etc.

This has been discussed for 20 years, including these posts:

Master items reappear after inserting new page

and

Move Every Object on Every Page Toward or Away from Spine

WOW! That’s amazing about the Fraction feature affecting that. But yeah, you don’t want that feature on for most of your text. All your numbers and stuff would get messed up. That should be off. (And then apply the Fraction opentype style just to the fractions that need to be affected.)