If you are bump starting (clutch starting) in such a way that you are putting more stresses on the engine than you would using the electric starter, then you are not bump starting correctly. Likewise with the wear on the clutch, input shaft, etc compared to down shifting (unless of course you don't ever down shift, or you double-declutch & rev match on every downshift). Bump starting can be done in a way that the engine would not know the difference if it is the key starting the car or the clutch.
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