I can only speak for myself and not the SOTT editors, but on those issues I have not formed a strong opinion based on the evidence that I've seen.
Certain videos show what could be pods, however there are lighting/ shadow issues that could be creating the appearance of something that is in fact not there. I have read the cases for pods vs. no pods and don't have enough evidence to accept either side. My questions on the pods theory are: Why would the pods be needed? Why use a plane with such an anomaly that would be photographed and analyzed with such scrutiny?
As for the flashes, I have heard the case for why they could be real and for why they could be electrical discharge or lighting anomalies. If there were real flashes that were intentional and planned, what purpose did they serve?
I think that summarises the problem with the theories well, to which I would add, what might motivate someone to promote these theories ahead of other elements of the attack, namely events at the Pentagon, where there is a great deal of evidence supporting something other than the "official story". No prizes for guessing.