Good question!
The Scale is not the Scale of the Cube, but of the Cube’s Coordinate System:

Also look at the Spreadsheet.
When you Apply the Rotation, you Apply the Rotation of the Cube’s Coordinate System:

The Scale of the Coordinate System doesn’t change, but the Position of the Cube’s Vertices (see Spreadsheet).
Confusing, right?
And yet so logical 🙂