Not sure what you meant by lower level mechanisms, but you can protect console logins and RDP with 2FA: https://duo.com/docs/rdp
Just think of any backend protocol that the system uses. The vast majority of those can't be 2FA'ed. This is not Windows specific either. The same is true for most all protocols.
This is why most companies buy firewalls and VPNs and only 2FA the VPN. That meets most compliance requirements and is simple to do. Is it secure? Probably not, but it checks the box (makes audit happy), so buy compromise insurance and move on.