Earlier quoted context omitted.
2FA can't protect you from malware on your machine.
Sure, but I wouldn't expect the vault to be accessible without 2FA each time it is cached. 2FA should be used as part of the decryption process even if the vault is cached.
Even if the 2FA was used for decryption, it wouldn't really make you much safer, because malware can steal the decrypted vault out of memory right after you type in the 2FA. A HSM would solve this, as long as the HSM has some out of band way to communicate with the user, such as an approval button that malware can't press and a screen saying what password to release.