@James Hamil Thank you for the case. This is now resolved.
The issue boiled down to a change I made to the name of my Azure domain back in December to update my sharepoint URL. This included adding a new "onmicrosoft" domain.
When adding the app proxy to applications in Entra, the blue banner at the bottom informs to add the CNAME pointing to the new domain (i.e. ilo-newdomain.msappproxy.net), but the CNAME needs to still point to the original domain.
Once we changed this, the certificates were identified correctly and the apps loaded correctly.