I believe Stephenson himself commented that the Enoch Root's long life and the ability to bring dead people back to life, both presumably due to alchemy, makes Cryptonomicon and the Baroque Cycle 'past sci-fi'. Otherwise, yes, it's almost the same as historical fiction. A perhaps better example of the blurriness between the two is "Gravity's Rainbow."

Anathem takes place on another planet, and in our future (in that characters in the book have our present as their past).