The beeping is the result of inaccurate GPS lock (which is 95% accurate to begin with). It beeps (to warn of the closing) when the system thinks you are not within the "garage location".
MyQ will send RF signal to close the garage in tandem with your car's GPS location BUT if the GPS lock on the car is not within the geofenced location of car vs garage (remember GPS is 95% accurate or worse if you have not moved or without clear view of the GPS satellites, like inside garages), the unit will beep as it closes.
Hint: After parking in your garage overnight before moving the car - go into the car's Service Mode and see how many GPS satellites are locked to your car and again just outside your garage. You'll see how good or bad GPS signal at your location.
Information about GPS accuracy
www.gps.gov