No, it can't. 2FA relies on the server side being in control and unmodifyable. Since Enpass works offline, all the necessary data and checks are on your machine. So an attacker can manipulate everything to his liking (system clock, etc.). Whatever second factor you choose, its secrets would have to be stored on your machine (as part of your vault) and would be protected with your password. Once this has been logged and the attacker has access to your files (which in your scenario he has), he can unlock the secrets and simply calculate the second factor. You gain no real security; you simply cost your attacker 5 more minutes of his time.