I watched the video and I did not understand why would they go to such lengths to use "alternative" mode most of the time, only using the proper one when in the NEDC cycle. Only downside I could understand from the talk is that it would use more AdBlue which seems such an unimportant thing.

Is there something I am missing?

Not only Volkswagen....

"In this paper, we described two families of defeat devices used in the Bosch EDC17 ECU to circumvent US emission tests. The first family of defeat devices was used by Volkswagen and lies at the heart of the Volkswagen diesel emissions scandal. The second device appears in the diesel Fiat 500X automobile sold in Europe, and has not beed documented previously."