1. He uses protein instead of calories to intentionally skew the numbers.
2.
a. He includes the initial deaths from clearing the land for crop use and doesn't really clarify that this is a one time deal. Or that by their continued existence many more animals will have come in to existence to die and suffer.
b. Also mentions annual killing of animals in the production of plant foods, but does not count the wild animals dying and suffering in grazing lands.
3. He focuses on environmental issues but from a conservationist point of view, which I fundamentally disagree with.
4. His arguments only involve cows which are the most humanely raised animals (imo), so including the other animals people eat only makes his numbers worse.
And as you mention, these people always use the best case animal farming and compare it to current sub-obtimal crop farming. If animal welfare became more prioritized then more humane methods of dealing with pests could be achieved in crop agriculture.