Normal makes sense for some primitives but not for others:
Scale[Sphere[], {1, 2, 3}] // Normal
Scale[Line[{{0, 0, 0}, {1, 1, 1}}], {1, 2, 3}] // Normal
Scale[Tube[{{0, 0, 0}, {1, 1, 1}}], {1, 2, 3}] // Normal
Your original file looks quite different if opened with version 12.0 and 13.3. I think that the visualization of Scale has changed in the FrontEnd with version 13.3.
