With ATHR engaged, and in VAV PTH with the speed window closed the aircraft will reduce speed as it crosses the speed profile points regardless of the flap selection. Unlike the Airbus, flap selection has no affect on speed control in the B787 and it's not new. It was always like this. The ATHR should prevent you coming below Vmin but you can end up with pretty high nose up attitudes if you are not careful. Airlines usually have an SOP which states an altitude below which the speed window must be open to avoid this trap.