I had assumed you were the producer of the video, which is a great video. If you are not and you look at the pump in the video it has a thinner cord, some earlier pumps had a much thicker cord and this caused the fit issue you describe with the bottom cover, this cord was overkill, it can be installed without the side or bottom bulge you describe but it is very time consuming and difficult and I just accepted the side bulge in my case as it was the easiest.
We always use this airgap design because it acts like a mute for the passage of air, the cup essentially is a silencer and dampens the wooshing noise, but I can see the potential problem you describe, the most common issue with this design is if the water level is too high the partial vacuum can draw water up into the air intake and reduce efficiency, in fact part of the design is that when the cup is removed some water should be drawn in to clean out salt creep in the air line, but it is less than perfect, cleaning salt creep with saltwater is not ideal.
We don't deny that anything we make could be better and we always are making improvements. I think you will find more than most companies we look to improve and take feedback seriously. We are however also a small family company with less resources and we can't always react as fast as we would like, sometimes we know something should be improved but we determine it is less important than another change to another product and we have to sort of pick our battles. So much of the 9002 is hand made that this also leaves a fair amount of room for human error, the basic shell of the body is an extrusion and the top and bottom pieces are molded, but every hole and thread and internal plates is installed and drilled or cut by hand. The assembly is very old fashioned with a lot of hand made wooden jigs to place the various pieces.