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.