They could keep the SE/E benefit of pre-boarding if they just wait until we are settled before they send everyone in. If a row 12 passenger isn't settled when you send the "rows 30 to 456" passengers in, then they will all bottleneck up in the aisle. If you wait till the aisles are clear and then send the masses, it will all go more smoothly. Also, checking to make sure that someone from row 20 isn't trying to get on with the 30-5000 people would help.
The claim in the article that someone who preboarded will then get up and try to interact with their overhead bin while others are still boarding is pretty laughable. I preboard, get in my window seat, and hide. My stuff is usually under the seat in front of me so I just try to shut out the chaos -- if I have something up there I do pay attention in case someone tries to move it away. Part of my "settling in" time includes extracting everything I intend to need from right then until the seatbelt sign goes off.