Why is lookism supposed to be bad/stigma, but favoring intelligent people is good/meritocracy? Both are "unjust" in the sense that they are a result of genetic lottery. If anything, it's the intelligence you are born with that you can't do anything about.
Society is better off with more intelligence, but also with more beauty! As we automate intelligence, the selection pressure on good looks will only increase.
> Why is lookism supposed to be bad/stigma, but favoring intelligent people is good/meritocracy?
Your question elides what “favoring” is in this context.
Outside of a few particular jobs, intelligence better predicts work performance, especially for knowledge work. The point of calling out the stigma of obesity is that it unfairly maligns people who are otherwise capable of contributing to a company.