Sooo… I found something interesting things…
With Connections disabled. On the WordPress Permalink Settings admin page, if I would select any of the default options ( Day and name, month and name, Post name ) the site map would only contain 2 URLs. The home page and one other one. Now, if I remove the trailing slash on any of the default options by using the Custom Structure, then all 62 URLs would be in the sitemap.
Bug in Yoast SEO? Unknown, but to my eyes it seems to be a bug and a pretty significant one.
Also, the sitemap did not seem to respect the selected permalink structure. Meaning the sitemap completely ignored the day or month (as examples) in the permalink structure and created the sitemap as if only using the post name permalink structure option. Bug or feature I couldn’t say. Seems like a bug though.
Now, back on issue…
With Connections enabled. I was able to get the homepage to show up in the sitemap. It was not being included because I need to filter the link and I added a trailing slash based on whether or not the user set the site’s permalink structure to have a trailing slash or not. Due to the first bug(?) in Yoast I mentioned the home page did not get a trailing slash and so was not included in the sitemap. I change the logic in Connections to always add a trailing slash to the homepage regardless if that was what the user set in the permalink settings or not and now it shows up in the sitemap. I do think this might be a bug in Connections because it appears the home page should always end in a trailing slash. Or it could not be a bug because the permalink structure setting should be honored. That’s difficult to know. I’d have to research further.
Anyway, I left the code in place which always adds a trailing slash to the home page for you to verify that it works fine now. I’ll very likely include this tweak in the next update to since it is a minor change which should have no negative effects.
I would encourage you to reach out to Yoast and inquire if the above to items I found are bugs or features.
I hope that helps!