I don’t think the problem is as large as you’re making it out to be. This concept is not unique to Blender.
This fundamental concept also exists in the other DCCs like 3DS Max and Maya as well. Over there applying scale/rotate/translate is called “Reset XForm” for Max and “Freeze Transforms” for Maya. Their “edit mode” equivalent is either called “sub object mode” in the case of Max’s EditPoly modifier or Component mode for Maya. They behave similar.
Object scale affects the object’s dimensions and those are simply different than the dimensions of the actual mesh data.
One concrete example: Model a table. ALT-D duplicate that table so that it shares mesh data with the first; i.e. it has the exact same shape. Now scale, in object mode, that second table to make it larger. This MUST be possible to do without also scaling that first table. And it is possible because of the separation of scales.