I manually updated the plugin-utilities.php file to read from categories.json and not site.json, and then updated to make sure it read the right json object (in site.json, categories is 1st level, and is 2nd level in categories.json).
However, I have 49 categories and only 33 are showing up in the categories.json as well.
So for the time being, I just manually added the one category that I wanted that was missing.
Still not sure if this is a max_category_nesting=3 problem, but even if it’s not, I think going forward wp-discourse polling the categories from categories.json may be smoother.