I was talking about MITM certificates. I don't really understand why a university is not just getting a certificate from a CA in the trusted store, but I would

I was talking about MITM certificates. I don't really understand why a university is not just getting a certificate from a CA in the trusted store, but I would have many fewer qualms about something that is not a general MITM certificate. That said, my experience is that generally applications that have a legitimate reason for a limited-use self-signed certificate don't need to be in the general store. For example, it's common to set up OpenVPN with a self-signed certificate, but I've never had to add a certificate to the general store for that - it's always app-specific.