The Boeing/FAA directive re: MCAS does not instruct them to extend flaps.
Further, there's other things going on in the cockpit due to the malfunctioning AoA sensor that's the root of all this.
Specifically one of the effects is that they get an Unreliable Airspeed Indication, and run that checklist. That checklists memory items include maintaining the current flap configuration (in this case, flaps up).
The Boeing/FAA directive does not instruct them to deviate from this and extend flaps. They have a checklist memory item instructing them to in fact do the exact opposite, and not touch flaps.