You have data and you have objects that contain data. Modifiers, and physics work with the data. Transforms are at the object level. So any rotation and scale at object level will sometimes appear to distort the mesh. That is because it comes after the modifiers. When you apply the transforms like rotation and scale you are actually making changes to the data. You can see this by using the default cube. Tab into edit mode and click overlays drop down and under measurement check edge length. You will see all edges are 2m. Tab to object mode and scale by 2. On n-panel it will give 4m as all the dimensions. Tab into edit mode and you will see that the data is still all 2. Tab out then add a bevel modifier. Scale on x by 3. You will see the bevel become distorted. If you apply the scale the bevel looks fine. That is because the bevel modifier works on the data.
