After watching episode 6x03 I don't think we have more reasons to suspect McAllister than we did before. What did or said doesn't prove anything. we can say he's RJ because we can see everything we know (or we are made to beleave we know) about RJ to discribe this guy!
Well no. We have not made any progress if everything he does or say can be also explained in a logical way. Why. Because then it's up to Heller to deside if he is RJ and make it happen.
Only things that could not be explained in other way than him being RJ, can be taken into account. Why? Because we have strange things for every other person in the show, that could be explained with that person being RJ.
So. What did McAllister did in this episode? CBI arrives at his jurisdiction and takes over.
The same happened in episode 1x02 and he was not happy about it, although he wasn't showing it much. Then he got emparased with Van Pelt and he didn't solve the case, Jane did.
So we expect him this time to be polite, cool, cooperative and not get in their way in a way they would get offended.
At the same time he has to show any way he can that he is sheriff for a reason and he isn't useless. And we all see that he does more than that in the end.

OK in the chapel Lisbon tells him to climb the ladder to get a hammer. Well nice is nice but he wouldn't do labor for these guys, he can get others to do work. So when he says about he would need other shoes, it's obvious that he is in the sheriff's shoes, and their errand boy. Look at the that scene. Can you see him standing like the authority he is?
Later at the cliff Jane tells him "come over here fela have a look". Well he is no "fela" he's the sheriff! Doesn't mean he's suspecious that he didn't go. And don't forget thet he was interupted.
From then on he is the nicest guy really. When Jane tells him he and his men need to hang back while Jane puts his plan to work, McAllister has no problem at all.
After he saves Jane he finaly tells him that he ignored him telling him to hang back, because he didn't trust them the way they forced their way to this case. He is still polite though. As for the pingeons flying to his face, well no one would like that.

Personaly I don't see anything suspicious about McAllister in this episode.

I've rewatched the episode 3 times now, ignoring the obvious clues/red herrings (fear of birds, middle aged, good posture, able to creep silently), and that one moment on top of the church, just before he extends his arm to PJ says a lot to me. In a body language sense, i read that he feels totally in control, almost as if he's sending a message to PJ, saying "I don't have to rescue you, i can kill you at any moment, but why spoil our game?"

.

Tom say to PJ

"hunter everything that has a face"

In the middle of the episoude S06E03 McAllister arrives with jane and lisbon at the "bella-vista" and he doesn't want to go there, maybe afraid of highs? NO.

When they arrive you can lister the sound of birds, so he starts looking to everywhere as you can see. He is indeed unconfortable there, then he left.

I dont believe that McAllister. But somehow he doesn't like birds.

That the reason he killed "Partidge" first haha

After watching 6x03 nobody seems to have mentioned the SHOES. McAllister is wearing the same style shoes as red john did in 'red sky in the morning'. It's probably nothing but I'm surprised nobody seems to have noticed as they even made a point of it as McAllister even mentioned his shoes.

Regarding the Psychiatrist-Profile of RedJohn: He has a real phobia issue, it remains to be seen if it is fear-of-heights.

Thomas McAllister obviously didn't want to climb that ladder in the church. He also didn't want to go to the edge of the bella-vista-view on top of that hill. Until that point I was convinced that he actually does have fear of heights (regardless if this makes him RJ or not). Bodylanguage and superficial excuses made me think so. McAllister communicated a fearful behavior.

At the end of the episode however he balances easily and completely fearless on the roof of the church to save patrick. This was kind of a twist in that episode. Now to Patrick and Theresa this fearless bevavior may rule out Thomas McAllister as actual Red John.

To me however it only proves that Thomas is very deceptive and manipulative. He really totally communicated a fear of heights. Yet he does not have it.

Such a discrepancy. Why would anyone --> fake <-- a fear? 

He overcomes his (faked) fear to save patrick. That definitely had an impact on him. Imagine someone afraid of swimming jumps into the water to save you from drowning. That does have an impact on a person.

We know Red John wants to be friends with Patrick. Now McAllister saved his life and even says "my pleasure, at your disposal any time".

When McAllister shoots the guy on the rooftop he says "Now he's talking directly to Jesus!". That made me laugh out loudly :) ... and then I thought: Well, he just killed a human being and is making fun out of that death and fun out of the afterlife. I know Police officers who use a gun for self defense and need a therapy afterwards. So again: A huge gap, a huge discrepancy in personality.

Furthermore: McAllister does have a very good olfaction, even better than Patrick. He smells the oregano at the dead body. And that "wrong Red John" who got shot in the shopping mall was told by the real Red John about the smell of Patricks Family. Well WHY the smell? He could tell some visual details or facts. Yet he talks about facts regarding olfaction. This is a little connection.

Last but not least: In that scene where Bertram, Reede Smith and McAllister sit in Bertram's office it is McAllister that offers Patrick "Call me Tom". That was the first time McAllister appears since the Season 01 appearance. He offers Patrick the hand of friendship: "Call me Tom."

I just watched the rooftop-scene again and the second McAllister helps Patrick back up on the roof he (only for a second) grabs his gun. And says: "Go!". That was an off moment. Have a look.

I don't believe it is Thomas McAllister, however so far we've had more hints towaqrd him than everyone else. In the latest episode, we learnt he was afraid of heights, people may argue that he was up on the roof at the end, but i think RJ would do anything to keep PJ alive, don't you? And just to add he was shitting bricks when the pigeon flew in! and who's afraid of pigeons? That's right,RED JOHN! Just as an extra little bit, probably insignificant, but when on the phone with Jane, he sounded a bit like Red John with a deeper voice! He was also able to read the dead guy quite well! Just my theory:-)