While I somewhat sympathize with Nakamura in that in case of AlphaGo vs Lee Sedol, Lee certainly had an "opening book", I disagree with your characterization that opening book is "usual". TCEC is widely recognized competition for chess engines and TCEC rule specifies no opening book. For engine-to-engine evaluation, no opening book is the usual method of evaluation.
One problem is that in a sense AlphaZero has an "opening book" encoded in its neural network weights. But just like it is unclear how to construct "Lee Sedol without an opening book" at all, it is unclear how to construct "AlphaZero without an opening book in such sense". So indeed, while unusual for engine evaluation, it probably is best to play against Stockfish with an opening book.
That's the problem. Stockfish has no opening book.
While there is no doubt Stockfish can play stronger with good opening book, keeping a book up to date with engine changes is really a full time job. So Stockfish project does not have any official opening book.
Personally, I think using publicly available Komodo book would have been enough, but obviously Komodo book is tuned for Komodo and everybody would complain about any book problem. In a sense, "no opening book" is the official upstream supported configuration, so it is entirely a defensible choice.
Fair enough (and thanks for dropping that knowledge bomb!), but it seems like they could choose whatever seems like the strongest configuration at the time. It seems like any opening book would make a pretty huge difference.
One problem is that in a sense AlphaZero has an "opening book" encoded in its neural network weights. But just like it is unclear how to construct "Lee Sedol without an opening book" at all, it is unclear how to construct "AlphaZero without an opening book in such sense". So indeed, while unusual for engine evaluation, it probably is best to play against Stockfish with an opening book.