The problem is that the test kit only gives you a single reading of the actual concentration of a substance in the water (which can sometimes be useful) but they do not give an indication of the flux of that substance through the system. The claim is not that there is more phosphate in the water column (like you say, it's either there or it isn't), but that the total amount of phosphate moving through the system (the flux) is higher than expected. Consider the following scenario. A tank is heavily fed daily, a skimmer or GFO is not used and little algae growth is observed. In that case you would expect the phosphate levels to be high because the input is high but the output (algae, skimmer, GFO) is low. This low output means the flux is low, so phosphate is allowed to build up. These might be conditions observed immediately before an algae bloom. Take the same system a week later and nothing is different except that there is now a large algae biomass because the high phosphate levels triggered a bloom. That algae is now drawing down all that phosphate. The test kit now reads low phosphate. But the tank is still fed heavily. The phosphate input is still high, but now the output is high too, so the flux is now high. Both of these systems have the same amount of phosphate going in, but one reads high phosphate and the other reads low phosphate.
If you looked only at the second system without any knowledge of the first, and tested the water for phosphate, and found it to be low, you might dismiss phosphate as the problem. That's because the reading is low but the concentration of phosphate in the water does not give you any idea what the flux of phosphate through the system is. However, the observation that algae growth is high indicates that the flux of nutrients through the system is also high.
