Why is it okay for the owner to do this, but not an employee? Why is it okay if you have just one shop rather than a chain?

For the latter, because that indicates a criminal enterprise. The idea of a coordinated group of people all breaking the law is deemed worse than one individual.

I can reconcile this with my own values.

Practically, an enterprise of criminals is more likely to be effective, and thus would create more negative costs.

Legally, it allows prosecution of the organizers of a crime group, who are likely the most dangerous and more difficult to catch in the act, as they contract others to do their work.

I am not a lawyer but in jurisdiction there may be a slight difference between crime and organized crime like between selling drugs on the street and leading a drug smuggling cartel. And training your employees how to break law could be also prosecuted.

Uber is being tried federally because their crimes cross state lines, which wouldn't be the case with one pizza parlor operating locally in one state engaging in the same behavior.

Uber is the subject of a federal criminal probe to see if they have committed crimes. Lets not get ahead of ourselves.

I'd think it would be more involved: They have an answering system that recognizes the caller ID. The IVR is set up to have an automated announcement report that the store doesn't sell alcohol or even that they are closed, and then produces a special ringtone, if the call goes through at all.

They claim it is to circumvent fraud (folks ordering pizza and not paying) and bad payments and the like as a cover. And it isn't just a local pizza place: This is a nationwide chain doing such actions.

Edit: Addtionally, employees would be trained to avoid such situations.