I believe OP is referring to the fact that a sophisticated attack has access to the hardware and you continue using it afterwards. They could, for example, change the unencrypted /boot partition to log the password you use to decrypt your partition. Or, if you sign the boot partition, they could install a hardware key logger, or do any other kind of hardware modification that defeats the security. Preventing this kind of attack is incredible difficult. They are many means to prevent those kind of attacks but, for the most part, it just making it harder for the attacker so that the attacker needs to become even more sophisticated.

Full disk encryption only helps if you are worried that your hardware gets stolen