As others have stated, I too found Tony's behavior bothersome in this podcasts. Emery only sometimes called him on it, so I agree with others that he should have done so.
Tony often used the non-argument of there being some "mystery" that we can't know. That's a real debate point, but rather is trying shift the burden of proof. It is a common technique in pseudoscience, and I heard it many times growing up about Catholic doctrine. Like "does the Host actually becomes human flesh?" Answer - "yes, but because we has humans don't have perfect understanding of everything, we can't explain exactly how, it's a divine mystery that you have to accept because of our imperfect knowledge."
So in other words, when the position is shown to be without basis, and no support for it can be found, the person simply claims that some unknown knowledge supports it, and since we can't get that knowledge, somehow we still have to accept the point. It's nothing more than a rhetorical trick that Tony used over and over.
It was good for Emery to call Tony on the rediculousness of the heavenly lobotomy, thus exposing the double standard of using "free will" to wiggle out of evil on earth, but someone keep sin out of heaven. It would have been better for Emery to cally that more strongly, because letting it go without explicitly stating that the view is rejected can be misinterpreted as sounding like you actually eventually bought the lobotomy explaination as rational.
The worst one, however, was probably Tony's mischaracterization of the idea that showing that one instance of suffering can be explained "invalidates the atheist's positive argument" and thus removes the whole logical theodicy issue. That's like saying that by proving that one food causes cancer proves that all foods cause cancer. All suffering need not be the same. If a criminal tortures someone, then that can be chaulked up to free will - but lots of suffering is clearly not free will, such as earthquakes, meteors, cancer (barring cases like lung cancer from smoking) and so on, with of course many in between. Tony's use of this rhetorical trick was never challenged.
I could go on, but I can see why many have suggested that Tony not be on the show. I would suggest that if he be on, he at least be called on these kinds of behaviors - which might make it a very good show, a lesson in how to have an honest discussion. I haven't listened to all of the shows, I'm coming up from the bottom with 1 through about 25, and 98-101. Others, like Norton and Scott don't do these kinds of things, at least not that I've heard.