https://www.flathub.org is using Let’s encrypt. Their certs only last 90 days so you need a script to make sure they are updated and pushed to your site. https://flathub.org uses Globalsign which lasts for 13 months. My guess is they don’t have a process for reconciling the two types of end dates.
Yeah, it isn't a good look for flathub. I looked at the certificate and the Subject Alternative Names section was missing the www prefix. Why they're not using Let's Encrypt and certbot beats me because this could all be automated.