Sorry for not getting back to this thread sooner but last week my
Ateca came face-to-face with a Cupra technician.
The technician had about an hour with the car and ran a load of diagnostics that all came back healthy with no issues. I completely expected this and thought that would be that. However, they have admitted that there is an issue with the car/keys, they have no idea what the issue is, but there IS an issue. They ran a few manual tests with the keys and changed the batteries (which were brand new) but couldn't get to the bottom of it.
The car has been rebooked in for the end of June so they can run extensive tests which will take 3 - 4 hours. They also want to run side-by-side tests with other Cupra's of different ages and models to get a better understanding of the fault.
Fingers crossed I can get some more information in the next few weeks that I can pass along. I'm not entirely hopeful but it's promising that they've acknowledged there's an issue and want to investigate further rather and just fobbing me off.