To be fair, doesn't all cooking alter food's chemistry? In fact, isn't that the whole point of cooking? Look at potatoes for example: humans can't digest raw potato, so we learned to cook it eons ago because that changes it into a form we can digest.
So unless I'm missing something related to terminology, he's right about microwaves altering food chemistry, but it's just scare-mongering because you frequently want to alter food chemistry.
The rest of those things you cite are, of course, total BS.