Primary concern of hashgochos is the reputation of their “brand.”
They don’t want their “brand” associated with things that the community Rabbonim will condemn or that ordinary people will chatter about.
They’re careful to not give hashgocha to anything that might taint their organization’s reputation (and market value).
Nothing to do with morals or even with halacha.
If you think it did, try complaining sometime that the heimishe supermarket is playing games with their scales or overcharging in some other sneaky way — “None of my business” will be the hashgocha’s inevitable reply.