I don't think we will know until much later. I think Thomas is going to sit on the shelf for a while. That guy in the cell isn't from the era of Merlin, whoever he is.
1. We have proof that the original Merlin traveled through time so we can't know when his era was or how often he skipped over parts of it by traveling to the future/past and staying there.
2. While he mentally "talks" in a Britishish accent, its all telepathy and as is said before Harry could just be "hearing" it and mentally assigning a British accent to it even without taking into account that Merlin very well could of time jumped to more modern British for awhile then returned to whatever time he wanted.
3. Jim will lie if needed to torture us so even though he said that Merlin is dead and that the guy in the cell isn't Merlin he could be lying.
4. Jim writes the fairies to be unable to lie but are masters at lying by omision, twisting words/meanings, and redirecting the conversation, so I wouldn't put it past Jim for him to say Merlin is dead and as in not breathing, eating, whatnot....kinda like someone who is suspended in status would be. After all Harry said that the Hunger wouldn't hurt his brother and with how bad his brother was at the time the only way that happens is by freezing him in time.
Also something I have thought before, in the real life stories Merlin was supposidly only half human and half fey or demon or something. So we have Mac who is shown great respect by very powerful entities ie Mab and Odin/Santa, as well as being called out by whichever walker. Mac who also healed superhuman (even to a wizard) fast after bullets were removed while he was unconcious and not able to control his actions. Mac who has been called Watcher with a capital W and who has stated that he's Out. Then we have who/whatever is in that cell. Could the occupent be the nonhuman part of Mac/Merlin? The bulk of his power locked away for some reason. I know that Harry has mentioned that he doesn't feel anything magical when touching Mac but if the bulk of his power is locked away in addition to the knowledge that Merlin had, its not that far of a stretch to believe that he could hid whatever remaining power resides within himself from a wizard.