i also built the same design......so does ati n aqualight. the purpose of using waterproof and caps is that u can actually wash or spray the unit for maintainance. its not meant to get so close to the water which what we intend to be so kiasu.
as for the commercial units, i do have wings so that is should be resting on the hood. from that, it will be @ 6-7inches above water so that it will avoid salt creeps.
the design is ok......yes, u cant fit alot of tubes with that kinda of design. but not everyone will need plenty of tubes.
cheers