Obviously, if you graze sheep / cattle / goats on marginal land, or even relatively arable land (jumping ahead to your op-cost comments) you don't have to transport food to them.
Transporting grain to feed grass-eating animals is not uniquely a north-American strategy, but is much less common in other parts of the world.
> Considering eating beef is much more energy intensive then eating the equivalent vegetarian diet, there's simply no way cattle farm is energy negative just from bacteria taking carbon from the manure
Eating beef, or raising beef? Again, if you focus on large tracts of relatively non-arable land to run cattle, the numbers are quite different than if you look only at land that can support nutrient- or calorific- dense crops.
I'd suggest Simon Fairlie's excellent 2010 book 'Meat - a Benign Extravagance' for some deeper examination of the logistics / numbers here.
Thinking about this a little more, I had it a somewhat wrong above. Most of the carbon that makes up the animal comes from the air in the form of photosynthesis. So if it's re-released back into the atmosphere, that's not a net gain. So I suppose to be completely neutral there would need to be an equal amount of carbon being sequestered in the soil to offset the factors already mentioned, like transport and processing. That does actually seem conceptually possible.
Rich topsoil is that which has lots of organic matter in it, i.e. carbon.
There are people who say the great plains were built by roaming buffalo herds, grazing on the grasses growing there.
So if that natural system was able to sequester carbon it stands to reason that humans could mimic it and in doing so also sequester carbon.