Doesn't look like the manager ever ended up asking anyone to leave and it doesn't seem he even knew his own store's policies on guns. I don't see anything indicating the store owner was against any kind of carry and it was just a problem that particular manager had.
He definitely asked him to put the firearm in his car. At that point he stated that he demanded a refund. So the manager was unsure what to do. The store owner appointed the manager to run the business. So any decision the manager makes is in full representation of the owner.