Not sure what you mean by "If the design team went with the software, there must be a reason." (Not doubting, just curious)
From what I've read the software changes put more stress on the emissions components so they're redesigned to be more robust.
There isn't supposed to be an impact on performance and economy with the phase 2 fix and by all accounts the DSG cars have been improved by the phase 1 fix.
Though, after the 265,000km warranty runs out these things might be time bombs.