One possible flaw in the episode is with the substitution of Roth at the time he joined the Naval Academy. As part of the Navy background to join the academy you have to provide your fingerprints. This occurs at the beginning of the investigation process, which occurred before the substitution.
Roth would have had at least three investigations to get to the level and compartment necessary for access to cryptology. At least two of those investigations would require taking his biological identification (e.g. finger prints minimum, retinal, iris, voice, etc). I know from experience the investigation units run independently and thus take their own identifiers and comparing them to the previous ones would be SOP.
While the episode makes the switch sound good, the substitution wouldn't work (especially in 2003 when he joined the Navy, being post 2001) as stated because of the biological identification taken before he joined the U.S. Navy. It would be in his FBI and DIA file at a minimum and subsequent investigations would check/compare the original as part of their standard operating procedures, especially for new compartments at the crpto level and even some renewals (every 5 years or so). Each investigation would run the risk of the new investigation team noticing the mis-match in biological material (fingerprints at a minimum) each and every time. Honestly, some investigations occur without you even knowing unless something comes up. I saw this occur to a friend who ended up having to tell everyone his Father was in prison. A review of the department caught this and the agency felt it could be used against him. By telling all of us it defused the possible blackmail and the investigation went on (at least he continued to work with us).