This scenario is also plausible: two different entities: Red John on one hand and the Three Dots Tattoo association (whiting the law enforcement) on the other hand. Red John is manipulating the Three Dots Tattoo association for his own interests and the Three Dots Tattoo doesn't know who Red John really is, but they want to know. Or they felt threatened by the Red John power.

Bertram clearly ask Patrick and Teresa to be informed, want to be there, to be the first to know. When Bertram, Reede Smith and McAllister meet together they doesn't show only preoccupation but also curiosity. They could easily kill Patrick if felt a menace but McAllister saved his life on the church roof.

Now I think Patrick Jane would manipulate in some way the Three Dots Tattoo association in order to reach Red John. The explosion could be a cover to hide Bret Stiles (wanted by FBI - Ray Haffner will acknowledge, he's part of Visualise) and the three most preeminent Three Dots Tattoo association which Patrick could use to catch Red John. 

Who is Red John? Hmmm....