Is it that you aren't understanding the tooltips? The tooltip specifically says that the scaling factor effects the "graph to the left", and that the value represents the level of light at which the graph is set to max brightness. If the tooltips aren't clear, I guess they'll need to be rewritten. Any suggestions?
If you turn on pond mode, with a sediment level of 0, and a light intensity of 40, it's the same as if you typed 40 in the "nrg per" text box for veggies. Sediment level should be relatively easy to see the effects of: look at the bar graph to the side of the pond mode. Set light intensity and the scaling factor to 40. Change the sediment level (probably manually, the up/down buttons seem broken) and you can tell the changes in light intensity at different depths.