if a single bot controller can buy up an entire stock of limited items legitimately, that is malicious as that company is not longer able to meet the needs of their consumers. That's bad for the company.
If it's profitable for anyone to resell, that implies the company priced below the market price and there would be a shortage without scalpers. So the company is unable to meet the needs of its customers in any event. Scalpers just make it somewhat more efficient.
It is illegal if the website’s TOS for making a purchase prohibits the use of automated software.
It doesn't matter if it's legal, it matters if the website owner doesn't want x doing y on their site. A bot consistently not abiding by owners' intent is inheritly malicious.
That doesn't make them right.