I tend to try to leave a door open if the key is in it. I don't totally trust it but it's never locked with the key in it.
You can program behaviour which I'm sure you haven't done with coding device which will automatically lock the car as you walk away. One of those codeable function VAG built in via coding.
Problem with that is it rests on the car keeping contact with the key. Duff kessy aerials will lead to it auto locking the car.
The
Ateca has been reasonably good at kessy behaviour. There were early Leon4 issues, that one seemed to be sleep mode was instigated on all doors, drivers doors isn't suppose to go to sleep to save the battery. Vag had issues with VWs in the early days. Ofcourse they might have instigated issues in reworking the software and hardware on Atecas.
Your dealer needs to fault check more, failing that they will need to swap out parts till they find the issue.