Have you done any "Wiggle" testing at the connectors to the items related to the codes? Clear codes. With the car running, wiggle thr individual connectors and see if there is a wiring issue.
Many things in the Industry don't always make sense. I have been in the business for over 40 years. I can tell you that I worked in the independent world for a long time before switching to the Dealer world. I never was a believer in better product or better diagnostic equipment until I...