This language in the rules book just further protects the passer by establishing them as a defenseless player. Passers were already protected by the roughing the passer foul. As a defenseless player, he can not be contacted by an opponent where the contact "is deemed unnecessary or excessive and which incites roughness." It also mentions specifically that illegal helmet-to-helmet contact against a defenseless player is grounds for a flagrant foul and a disqualification. Basically, the margin for error with illegally contacting a defenseless player shrinks dramatically.
To be completely honest, it doesn't change all that much. Passers were already protected, and helmet-to-helmet contact against a passer was already grounds for a flagrant foul. The committee was asked to provide a few examples of who are defenseless players because a list didn't exist in the book until this year. The passer was just one of those examples added in.
To answer your specific questions, defenseless players are allowed to be contacted, but the opponent is responsible for contacting these players legally and must not be deemed excessive or unnecessary. A passer can still be tackled, it just has to be done legally, i.e. not hit with the helmet, not hit above the shoulders, etc.. A fake pass is not "in the act of throwing" because there has to be an attempted pass to be in the act of throwing. A fake is not an attempt. Nothing is preventing a QB from faking the pass and taking off, but they are not considered defenseless or a passer by rule, meaning they are not protected.