Well, yes and no. You should be able to run the pump down to an empty tank and it won't harm anything - if the tank doesn't have a lot of crap in it. What happens in reality is that contaminants that would not normally be picked up by the pump start to get sucked in when the tank gets really low. So, when you run the car low on fuel, then the stuff tends to get sucked into the pump, which can cause it to fail. This happened to me in Vegas with a BMW 3-Series - we had to change the fuel pump out in the parking lot of the hotel with a full tank of gas!
Boxster fuel pump replacement article here:
Pelican Technical Article: Fuel Pump Replacement - 986 Boxster (1997-04) - 987 Boxster (2005-08)
-Wayne