@ngrmm I did what you suggested and installed the new module locally. It has more fields on it than the old one and I tested adding settings specifically to the templates for the pages that are missing and then added a priority of 1 to them which seems to be the only thing I can do for when they're not showing (the rest of the options are for hiding pages that are in the sitemap), but I still don't get the pages showing.
The way things are set up is like:
- Shop
--Categories
---Category 1
---Category 2
--Product 1
--Product 2
So the /shop page and all the products directly below it show up in the sitemap, but the /shop/categories page and all its children don't show.
I can't see anything in the settings for the templates for the categories or the children or the pages themselves that should be hiding those pages.