Hi @pattybhat ,
In general (there are exceptions of course), to put it simply:
When it comes to Meshes, it is always best to Scale in Edit Mode. If you ‘forget’, or are too ‘lazy’ to switch to Edit Mode before, you can Apply the Scale after Scaling in Object Mode. So it’s pretty inconsequential which you use.
Having Proportional Editing on when Scaling, would only be a problem if you Scale in Object Mode.
Auto Merge has more dangers that advantages in my opinion (and thus I never use it), but can indeed give different results when Scaling in Edit Mode vs, Object Mode.
So:
Scale in Edit Mode, or Apply the Scale.
If possible, Rotate in Object Mode (and avoid Applying the Rotation).
