Students do get confused by this. First they get to understand the aircraft is flying in a parcel of air and that what the ground is doing is irrelevant (Shaggy's "above a layer of stratus scenario"). But then they have to partly unlearn that - when they start learning to land in a wind gradient and are told that it takes time for the aircraft to respond to the changed wind speed so that the air speed (momentarily) changes.
No, the ground IS still irrelevant, you are not UNLEARNING anything, but learning a new bit, that you are still flying in a parcel of air, but that parcel is changing ( or another way to think about it is that you are moving from one parcel of air to another) and you need to allow for these changes. The ground
may the the thing that is causing the change and this is good because this can be anticipated, but there are
other things that can cause a change such as CBs, and other weather phenomena and these cannot always be anticipated in the same way.