This is the change to the portion of the script that looks for encryptable volumes. Part of that script determines whether BitLocker is already encrypting a drive and, if so, MDT then makes the assumption that it must be doing an upgrade and merely has to re-apply protectors to a drive at the end. In reality, this gets tripped by the fact that the external USB disk is BitLockered (the MDTDEPLOY partition). This results in a failure during the final BitLocker steps since the TPM doesn't get owned and, therefore, cannot be used for enabling protectors.
This change is around line 1350 in the MDT 2013 Update 1 version.