The whole idea behind the drop checker is that it circumvents the exact situation you are describing. You want to use the KH-pH-CO2 chart, right? But to use this, you need two things:
- An accurate measure of pH
- An accurate measure of KH which also has to be purely carbonate or bicarbonate in source
Because of these two requirements, you can't use your aquarium water for the measurements. This is because several substances can act as buffers in the water column besides carbonate and bicarbonate. You can probably measure your tank's pH to some level of accuracy, but the harder problem is determining the "real" KH of your tank water. The test kits usually only measure the KH contribution from carbonates.
You overcome this problem by filling your drop checker with a "known" solution. Your drop checker should be filled with a solution of deionized water that is prepared to have a KH of 4dH using sodium bicarbonate (baking soda) -- to this, you add the pH indicator drops. And to clarify further, there should be an air gap between this "solution" and your aquarium water. Your aquarium water and the solution should never mix.
Because you know the KH of this drop checker solution, and because you know that the buffering is purely from bicarbonates (because that's all you added), then you can use the KH-pH-CO2 chart. Obviously, you get the pH from the color that the drop checker solution turns to after there has been sufficient time for the CO2 to diffuse from your aquarium water into the drop checker solution.
Therefore, using the drop checker in this way, it doesn't matter what's in the aquarium water column: peat, tannins, PO4, diet coke, etc. That's exactly the point... all the variables have been removed. Just make sure that the drop checker solution really is 4 dH and that you calibrate your pH kit so when reading the color you can determine the pH from the chart.
Calibration is the process of creating known pH solutions and then seeing what colors you get when you use the pH test kit. As an example, see this post where I calibrated a Nitrate test kit.