True enough, but on the other hand, I'm not really concerned with the feelings of fat villains, because they're fictional. I'm concerned with the feelings of real people who are overweight for any number of reasons, and who are frequently hurt both by negative comments about body size, and by representations of heavy people as greedy, evil, or disgusting. So regardless of whether or not there is a valid "in-universe" reason for a character to be fat, my attention is focused on how that representation is reflective of circumstances in our own reality.
The equation of bodily fat with gluttony and greed is, of course, a valid narrative trope, as you point out. But just because it makes sense doesn't mean it's not potentially hurtful. Any author has the right to use whatever characterizations or narrative devices their particular narrative requires in order to work, and I firmly believe that. But an author who intends to use a characterization in a way that could contribute to an existing social system of degradation and belittlement should, in my opinion, consider very carefully whether that characterization is actually essential to their narrative or not, and whether it's worth the potential cost. My suspicion is that many of these "fat bastards" we've seen in literature to date are the result of not considering those questions closely enough.