ATS does not replace Skimmer, as they do not do the same thing.
a skimmer removes organics before they have a chance to break down into N and P, that is surface active organics which are like 20-30% of total Organic carbon (TOC)
ATS promotes growth of algae (any type) which removes N and P from water. in turn the scrubber's algae releases all sorts of vitamins and long and short chained organic carbons, which will lead to promotion of bacteria growth and increase in their number and therefore increasing what can be skimmed out via a skimmer. the Skimmerless ATS tanks all crash for no reason after 2 years ! TOC overload? maybe, I have never seen a successfull SPS tank using ATS so ...

according to many, the extra organic leads to population increase in bacteria (good and bad) which can deplete Oxygen really fast in a closed system . and can lead to coral death. (tht is one way algae combats corals for space

)
http://www.sciencedaily.com/releases...0612221839.htm
From it :
"Our study shows that bacteria are the front line that kill corals," Smith explained. "Algae release sugar, fueling bacterial growth on the corals. These bacteria suffocate the coral by cutting off the supply of oxygen. Once the corals die, this frees more space for more algae to grow. We think this process sets up a positive feedback loop that accelerates the rate of decline in already damaged reef ecosystems."
sorry if this is not that related to topic at hand
regarding over skimm, please correct me if I am wrong., but certain elements like copper and iodine attach themselves to organics and therefore get removed that way. which can cause Issues

over-skimming a SPS tank could make the SPS fade in color, I THINK due to elements, as studies show that a skimmer, doesnt matter how big, cant remove none active organics.