Basically what the text says is that plant-based food usually is less resource intense and thus better for the environment, but there are also other factors and plant-based food production isn't perfect. (Independent of the question whether all the other things he says are true.)
So the headline is obviously strictly true, but highly misleading. A more accurate one would be "Vegetarian diets are good for the planet, but they're not the whole solution".
The text explicitly says that vegetarian diets are not part of the solution. Either now, or under the system he proposes.
He's very clear that eating a fully vegetarian diet now is worse, footprint-wise, that eating a mildly omnivorous one.
He's also very clear that while eating a vegetarian diet under his proposed system would be just about possible, it is built around the assumption that most people will be eating meat, and that it would form a primary food source for the months of year when plant-based sources were scarce.
He's certainly trying to suggest that vegetarianism is worse, but he doesn't back it up. In fact, his off-hand remark that "Most of these staple crops — especially corn and soy — wind up in animal feed" undermines this point.
"He's very clear that eating a fully vegetarian diet now is worse, footprint-wise, that eating a mildly omnivorous one."
I don't think the article ever mentions that point of view. This is the only time a similar argument is mentioned:
"Given the way we grow food today, it’s more accurate to say that vegetarian diets are “less awful,” not “better,” than omnivorous diets"
The only time a mention of an omnivorous diet being an improvement is under the constraint that produce is bought locally, perhaps at a farmer's market:
"A vegetarian who consumes whatever’s in the produce aisle of Wegmann’s is going to have a much larger eco-footprint than the plant-centric, meat-occasional omnivore who purchases exclusively from the local farmer’s market"
Frankly, that kind of consumer has to be in the extreme minority.
There are many facet to preserving the planet and optimizing food production so the jury is still out.
One quick interesting discussion point is that no land can indefinitely sustain intensive farming and some plot will only ever be able to sustain grazing animals.
So let's reduce these constraints for the sake of argument: the world is two field as such. what's more eco friendly? A corn farm and a shrubland, or a forest and a sheep herd?
Basically what the text says is that plant-based food usually is less resource intense and thus better for the environment, but there are also other factors and plant-based food production isn't perfect. (Independent of the question whether all the other things he says are true.)
So the headline is obviously strictly true, but highly misleading. A more accurate one would be "Vegetarian diets are good for the planet, but they're not the whole solution".