There are two schools of thought on the CO2/aeration issue. I had a private discussion with Tom Barr on this some time back, when I first noticed some sources (articles in TFH and such) beginning to recommend aeration to increase CO2. There are to my knowledge no determinable studies yet on the results, and the atmospheric aspect was Tom's main point too.
I assume your "agree except on the CO2" is in reference to my previous post. Tom's point was that there can be a lot of CO2 in tap water [you can do a pH check of your tap water straight from the tap, then after vigorously shaking it, to see the difference if any which will give you a rough idea] and this enters the tank with the fresh tap water. This gets used up or dissipated over a period of hours, after which the CO2 is at a lower level until the next water change.
You do not want to aerate too much overnight, unless you have a CO2 problem for the fish. The idea behind natural or low-tech systems is to allow the CO2 to build overnight so the plants can use it when the light comes on. I have been experimenting a bit with increasing surface disturbance, and things have actually improved. Of course, this is permanent, the disturbance I mean, day and night, since it is due to the filter return agitating the surface a tad more than previously. I went to this because I did actually notice some of the fish respiring more after the lights came on, and increasing the agitation has resolved this, so clearly there was a CO2 imbalance. This is something you will just have to be aware of and keep an eye on, when fish are in the tank; the whole benefit of soil is initial CO2 production, so obviously this will be significantly greater (or should be) with soil for the first 6 months or so.
Byron.