Actually, it does account for the effects of plants, etc, but only in retrospect. That is, it creates daily rates of increase/decrease based on your old water change schedule and your current (normal) substance levels. Thus, it basically uses the following logic: If your aquarium normally has X amount of a substance and your previous water change schedule was Y, then your daily rate must be positive if the normal level exceeds the amount added by the tap water and the daily rate must be negative if your normal level is below the amount added by the tap water.
The net result is that you can not plug in something like "I want to add 20 plants," but you can buy the plants, complete a few water changes, and measure the result by plugging the new water test results into the spreadsheet. The differences in the daily rates will show the effect of the plants. No less, that is kinda tedious and...pointless.
As it stands now, the spreadsheet is designed to only handle the effect of changing your cleaning schedule, no more or less. Sorry for the inconvenience.