Why/how does the Nav system interact with the phone? It was once explained to me that in-car Nav was worth the added cost because it would work where there was no cell service. The Nav in my allroad worked well, but the Atlas seems to have different hardware and software and it is awful.
That "selling point" is just a sales guy doing what they do and utter bull stuff

If you were ever in a place and starting the nav fresh without any cell data.... the car would still be running off of the ephemeris it had from prior. Nav does not have another way to get the information other than the pipe coming over the cells data slots. If the car net does not have any assistance the on the initial location fix will take a lot longer. If your lucky maybe 10 minutes.
The nav will work by itself without the mobile (using the same thing that the Car Net uses) but when the mobile is plugged into car play it is the device that provides the mapping even if not in car play. Does not make a lot of sense. The module where i plugged in down in front cubby was what was causing it on both maps (car and iphone) ... it would make my device and my car way off.
Here was my previous and it worked ...no problem since and it was simple enough i could do it.
This was so simple and even as a person who was a LBS/AGPS SME for last 15 years it really surprised me when i fixed it accidently due to the Apple Play not working anymore for audio.
I have had the issue on my 2020 Atlas Cross Sport SEL R line
I was having the navigation issue with device and car play showing i was driving in the sound or over mountains according to the maps on my car and also on my phone when it was plugged in to the car. Recently the usb plugs in front have been broken physically, it seems it had been coming for a while. I purchased a replacement USB hub and installed. BOOM ... both my phone and my car navigation work with no issues. I would have never replaced had the usb become unusable.
The interesting thing is i used to have to unplug my phone from car in order to get maps to work right...
Anyhow this seems to be the root cause. The usb plugs in front cubby need to be replace. 140 dollars and i put it in mysel. It makes sense at a 1000 feet but the issue that was happening in that hub to cause this, i do not have the knowledge to figure that one out as i am unaware of how the signal is used in the Nav Center of the car. This tracks out as well as i have seen that people that used bluetooth connection instead of cable were able to fix as well.
Sorry for the poor grammar...this site kept giving me fits