You could look into apps like authelia, keycloak, authentic, etc.

linuxserver.io have a templates for Authelia and Authentik on nginx

https://github.com/linuxserver/reverse-proxy-confs

Some systems support MFA eg vaultwarden. For that I use the built in MFA with Yubikeys.

For things that are not MFA supported but I need them to be open I put them behind Authelia and Nginx Proxy Manager.

Authelia config makes sense now. It was confusing at first however the custom config required on NPM still confuses me.

Anything else stays off the internet and I can access via vpn back into my LAN.

Not sure if it fits your requirements exactly but I just put a service behind TwinGate and it works well for my usage case. I can allow my wife secure access to services she needs to access from anywhere securely - she just opens the app to connect and she can access what she needs.

I haven’t but you can enable 2FA, as well as restricting based on things like hardware, OS and whether a device has biometrics.

If you're comfortable with using Cloudflare, you can use their zero trust tunneling and setup an application layer that adds auth to those services. I have mine protected by my GitHub login.

I used to run Authelia with NPM. It supports TOTP as second factor.

It is! I know that Mastodon and Lemmy support it. I cannot speak for any of the others though.