He mentions that the Average meat eater also is more likely to do certain bad things for the gut: alcohol, white bread, etc - that that's the "average" meat eater, not all meat eaters. Some people who eat meat do'nt consume things like alcohol, white bread, etc - and so the study hasn't controlled only for "eating meat" - Kresser's comments on that seem right on.
A related point is that being vegetarian doesn't necessarily mean the person eats vegetables. Seems obvious, but think about the effect on the microbiome.
So the real study that needs to be done is something like "how many ounces of vegetables do you eat per week" and compare that to the gut bug test results, without caring about whether the person eats meat or not.
Someone who eats a LOT of vegetables, and also eats small amounts of meat, logically isn't ruining the good things all those vegetables are doing for their microbiome. (as long as quantities of the meat aren't high enough to aggravate ammonia or reduce the quantity of vegetables the person consumes, and assuming there isn't some "bad bug" in their gut that thrives on small amounts of meat) Therefore, the fact that there exists any meat at all in the diet doesn't correlate with health of the microbiome, instead, it is the quantity of vegetables eaten that matters.
I run into people at my job who discuss all sorts of diets they are on, and some vegetarians/vegans seem to live on almond milk and grain cereals, nuts, fruit juice mostly without pulp, and vegan protein powder - no vegetables at all. That doesn't seem like it would support a good microbiome, although it is vegetarian.