I believe Red John pulled a "Patridge" and faked his death during the explosion.
Something feels off about todays reveal, unlike most people here i will wait for the explanation for why and how Betram is Red John but Patricks attitude to it it all made me think that he didn't quite think it all fit together in his mind either.

Unlike Patridges death, where we saw his dead body the other 3 suspects are believed to be killed in the explosion as dna evidence is found but the key part here is that cho said the bodies couldnt be identified cause they were burned to a crisp.

Another note is the storage locker which Bertram took the items from belong to Thomas McAllister as the attendant there referred to him as such after seeing his storage access card.
We also saw that a thumb drive was in the storage and that it 'probably' contains a list of all corrupt law enforcement officers and officials.

The question in my mind is why would McAllister be the one with the list of corrupt Agents if only Red John would have access to it as he is the leader of the group.
I think that Bertram was told by McAllister to collect the items from the storage to help aid his escape (incriminating Bertram in the process) and that he also left the swat outfit for bertram in his house so that all the attention would be on Bertram escaping and being the only available Red John suspect.