Why is everyone so hung up on encrypting a boot record, anyway? The purpose of encrypting these disks is that one cannot take a disk away and gain access to the data. If someone had physical access to a system, where they could alter the system then put it back in place for the owner unsuspecting owner to use again, the encryption system used is not the problem. Given that level of intrusion, passwords and even biometric measures are likely to fail to protect the data. I'm not sure a secure token would be enough for that dedicated a hacker.
For less drastic protection, allowing the boot disk to load up the encryption algorithm and present a challenge and password should be sufficient. It would be very easy to configure a USB key to be the boot device for a system, and have the boot sequence mount the kernal from an encrypted disk. No MBR on the root disk at all, so the entire disk could be encrypted.