Well there were / are assorted boot fittings. Not sure of the model you say. The well is really designed for a skinny although you might investigate the height adjustable boot fitting which may lift the cover sufficiently above a full size wheel. There is a pinned thread on fitting one of these also on the
Ateca side the standard fitting for a skinny with the panel. See both pinned threads in the standard
Ateca and
Cupra Ateca. Interchangeable between the two. One covers installing the standard floor the other covers the variable floor. The latter might give you the height.
It's a tape measure job. Perhaps someone with the variable floor can measure it up and comment.
It seems some of the parts least on the boot floor aren't available from Seat now, but are from Skoda where the Karoq is the same physical car. Worth looking out for. Need someone with a tape measure and take from there on wheel size. Failing that you can put a skinny in. They are basically the Leon 3 skinny.