Yes, at the end of the day you're going to need to move stuff from non-air-gapped devices to air-gapped devices and vice-versa. You can assume the non-air-gapped devices are completely compromised. But why is the air-gapped device not configured to always show file extensions?
This is literally working because Windows is configured to hide common file extensions, and the attack relies on hiding a folder and replacing it with an executable with a folder icon and the same name +.exe.
If you're designing an airgapped system, this is literally the first thing you should be worried about after ensuring that the system is actually airgapped.
At least windows explorer should have been configured to show extensions (and some training delivered to ensure that the people using these systems have the diligence to notice unusual file extensions with familiar looking icons).
It would be even better if the file explorer was replaced with something less easy to fool. Something which does not load custom icons, never hides directories, and maybe even prevents access if the flash drive has indications of shenanigans (unusually named files, executables, hidden folders) which would indicate something weird was going on.
It's a good job that unlike with Stuxnet nobody plugged in a flash drive from the literal car park, but this is pretty poor on the part of the people designing/implementing the airgapped environment.