You wont get a wet floor with any type of set up if you set it up right (unless of course your tank physically breaks, leaks etc.), the worst that will happen is your pump will run half dry and the tank will have a little more water than usual. The only problem that may arise is your ATO might continually pump in RO water which MAY overflow or lower your salinity. But again with a high quality ATO this can be avoided since some have an auto shut off function if it runs for an abnormally long time (the Tunze Osmolator is an example).
Leave about an inch or two of water space in your main tank and have a small separate overflow section of your sump for the pump. That way if water stops coming down the pump will exhaust the special place for it, but since no water is coming in it will have only added a gallon at the most into the tank, plenty of room up there to take care of that. And vise versa, if water stops going into the tank, as long as the drilled holes, overflow box, or pump is in an overflow section of the tank and can only skim the top layer of water, the few inches in the sump can take care of it. If there arent overflow sections even with a drilled tank you can get a wet floor. Just design it right and you should be fine.
Still, drilling is the best way to go as it is more reliable and you probably wont come home to a half dry running pump every few days.