You can use FIDO tokens for other protocols: I use it for SSH, for example since OpenSSH 8.2 or so.
On the other hand, you can configure mutt to use a client side TLS certificate and SMTP servers (e.g., postfix) and IMAP servers (e.g. dovecot) both support client side TLS certificates without having to support sending HTTP requests or parsing HTTP responses.
https://fidoalliance.org/specs/fido-v2.0-id-20180227/fido-cl...
OpenSSH uses that protocol to request encryption operations. Mutt could do that the same way but it’d need a server which supports the same crypto algorithm FIDO2 specifies. That’d be great but also somewhat pointless if you’re using Yubikeys which support x509 auth which IMAP and SMTP have supported for decades.