I see no cause to be concerned about flour on the finished bread. It’s pretty routine and is often used for decorative purposes.. Unless you are objecting to the aesthetics of this particular loaf.
I can no longer find the reference to the bubbles on the crust. I know I read about it and I believe it was an aesthetic rather than anything too serious. I will look some more and see if I can recall in which section it might’ve been. Damn I hope your books make it today. Amazon does not seem to have lived up to its usual reputation here.