Purely from personal experience (I know, I know), Flask's Python 3 support is solid. With a little bit of intuition, I'm sure any Py3-related problems from following the book could be worked around.
Since this book is meant to provide practical advice, I think it makes sense to write with the assumption of Python 2. Specifically, I’ll be writing the book with Python 2.7 in mind. Future updates may very well change this to evolve with the Flask community, but for now 2.7 is where we stand.