Flatness on molded parts is an almost impossibility to asses due to the the many variables associated with the cooling and setting process.
Also flatness of one side may be affected by the other side. How are you supporting the part to be measured on a single-side?
Once points are gathered by whatever means, I think you are going to require some statistical analysis software to arrive at a QC-usable figure to test for flatness of incoming production parts.
This quest falls closely aligned with the knapsack theory and people have spent lifetimes trying to resolve those conundrums.