If you use non-uniform scale outside of sub-object mode, it's going to distort the local transform space of the whole model. If you need to scale stuff, best to do it on the sub-object level: Vertex, Edge, Polygon, Element, etc.
lets approach this another way. The cube above has 8 verts right? 4 verts are filled with a polygon. Every polygon is made from triangles. say you have 5 verts being filled. This is 3 triangles to the engine. Lets say you have 8 verts as constructed as above, this is 6 polygons or 12 triangles to a game engine. But in…