mbsync (isync)
UseKeychain yes
Add the above to mbsync configuration and create the keychain item with:
security add-internet-password -r imap -s Host -a User -wmsmtp
Use the exact host and user configured in .msmtprc. The process is automatic if you got these right and have compiled msmtp with macOS Keychain support.
security add-internet-password -r smtp -s mail.freemail.example -a joe.smith@freemail.example -w