He definitely is red John. If you recall the lines red John whispered to Jane when he was tied to a chair and red John had to come and rescue him from the killers..he quoted a few lines by William Blake. And after an interview Bertram too quotes a line from William blake's work to Lisbon. Dunno if it's connection enough to deduce that Bertram is red John. And obviously the other things too fall in place like the fact that he is in CBI and he also is a plausible suspect in burning Todd alive. He was near the room. And another time when red johns lover (alleged) was poisoned they show a robust and huge guy coming from opposite direction in a view that was shot from behind the guy..that definitely makes it plausible that Bertram is the guy.