I don't disagree. It is, as I say, a way to add some extra flexibility. If it wasn't specified to have a back-up engine, I wouldn't be suggesting we add one, but since it's there, well, it's not a bad thing.
What I would add is that commuter EMU stock tends to work on more rigidly defined and shorter routes, IEP is going to be travelling over a much wider area with more diversionary routes, it's going to be encountering rolling electrification works, and circumstances could well result in very unusual train configurations, such as 5 car bi-mode units having to haul 5 car electric units in passenger service - that only can happen because the electric unit has its back-up engine.
It's also quite possible that future generations of EMU have battery back up power when density, safety and mass issues resolve themselves. It's tricky to fit battery packs or diesel engines to 20m EMU stock right now - ThamesLink tried with the Class 700s and sort of ran into a brick wall.
Indeed I see where you are coming from there. And as najaB suggests if they are coming out of a common engine pool then the costs would be significantly reduced.