Welcome to EE!
Your measuring method sounds complicated and I am not sure what your'e measuring or the accuracy of the method. -- Which is why the engineering folks are questioning you as well...
I would explore a measuring method that is easier for us engineers to understand...
Ultimately the lower frame of your feature control frame controls the features to within tolerance boundaries that are located at the basic dimensions to each other and oriented to any datums referenced. Since there are no datums referenced in the lower frame I would come up with a SIMPLE method to measure directly from feature to feature.