The boot verification code wasn't replaced, because it sits in the encrypted partition.
Notice that if they can modify/replace the device without you noticing then they can leave you one that displays the same unlock screen as the original but sends any credentials you enter to the attacker. Once they've had physical access to the device you can't trust it. The main advantage of FDE is that they can't read what was on a powered off device they blatantly steal, and then the last thing you want is for the FDE key to be somewhere on the device that they could potentially extract instead of on a remote system or removable media that they don't have access to.