For me, I don't think that the application is public exposed is really the problem (i.e. not in intranet).

I think the real problem is that these applications (Entra ID) are multi-tenant, rather than a dedicated single-tenant instance.

Here, we have critical identity information that is being stored and shared in the same database with other tenants (malicious attackers). This makes multi-tenancy violations common. Even if Entra ID had a robust mechanism to perform tenancy checks i.e. object belongs to some tenant, there are still vulnerabilities. For example, as you saw in the blog post, multi-tenant requests (requests that span >= 2 tenants), are fundamentally difficult to authorize. A single mistake, can lead to complete compromise.

Compare this to a single tenant app. First, the attacker would need to be authenticated as an user within your tenant. This makes pre-auth attacks more difficult.