I-9 manual is for employers. If employer has checked that your I-765 pending for 90 days, employer has fulfilled the obligation and can let you work. By observing this, you employer will not be punished by immigration law for hiring illegal person. They are probaly 100 types of categories about alien work authorization, Congress don't expect employer to be immigration expert or to hire immigration lawyer everytime employer hires a foreigner. That is what this I-9 manual EAD language is about.
The alien, on the other hand, should know about his own specific EAD category and limitation. The status examination during I-485 adjudcation should review your status and work authorization since you last lawful visa admission, and your EB I-485 is only approvable when such illegal violation days is less than 180 days.