How can something which is horribly inefficient for environment (water use, land use, greenhouse emissions from fertilizer) possibly be S tier?

What a weird question, if it was at all genuine. Not only is it not inefficient but, e.g., cows are absolutely unique and amazing for their ability to digest, e.g., grass into something that is highly nutritiously desirable for humans.

Meat especially grass fed beef, is not just protein, it's an incredibly dense source of nutritients. You have to eat far higher quantities and ranges of plant based alternatives to acquire the same nutritional value, and they are usually less bioavailable. So from the perspective of the person consuming it, it's very efficient source of nutrients, and also the most satiating food you can eat, so you won't feel the urge to overeat.

Abstractly, using land for crops is around an order of magnitude more efficient when considering only calories per unit area, but when considering the total system i.e the humans consuming it, there's an argument to be had that more livestock could be more efficient when considering all the side effects of a huge population of malnourished humans overeating refined hyper-paletable carbs.

For either side of this argument, the real issue is industrial agriculture producing both crops and livestock in unsustainable and nutritionally devoid ways, that are incredibly bad for the environment and humans consuming it.

Because that's not what we are talking about.

Biodiverse farms with animals and plants, rotating crop fields, are far more ecologically friendly than pure plant farms.