My claim is that Headscale has a lesser likelihood of compromise than Nextcloud, and that the E2EE provides an encrypted channel between nodes without an immediate need for TLS. Of course TLS over E2EE enhances CIA. There's no pushback to defense in depth here. But in the beginning, the E2EE will get them moving in the right direction.
OP began the post by stating that the login page to a complex PHP web application is internet facing (again, yikes). Given the current implementation, I can only assume that OP is not prepared to deploy a CA, and that the path of least resistance -- and bolstered security -- can be via implementation of HS+TS. They get the benefit of E2EE without the added complexity, for which there is plenty, of a CA until if/when they're ready to take the plunge.
If we're going to take this nonsense all or nothing stance, don't forget to mention that they're doing poorly unless they implement EDR, IDS, TOTP MFA on all services, myriad DNS controls, and full disk encryption. Because those components don't add to the attack surface as well, right?
Or we fix some shit at home first.