Dr Haskell did point out that when there is damage to they thyroid, such as scar tissue, these folks may have to stay on thyroid medication and he does mention dessicated thyroid as well.
You mentioned that even you have to take some thyroid in order to feel better due to damage.
I really don't see how what he is doing is contrary to what you are saying, other than he likes to use a synthetic compounded thyroid med, instead of natural thyroid (due to thyroidperoxidase activity increases) that he sees with dessicated thyroid hormone.
He explains that this is the process that he found to work, so he is not saying it is the ONLY protocol. He does introduce Iodine after the selenium has been taken for a couple of months to build up their stores.
So again, I do not see how what he is saying is so contrary to your protocol.
I think he provides a simple enuf explanation regarding the thyroid in Hashi's for those that would like to know.