Mighty Gem,
If I understand your issue, it is that you feel that the seat's centroid, as you have estimated it, and the pilot's position in the seat leave the CG at different places than that which is calculated when using the procedure in the weight and balance section of the flight manual.
I suggest that you follow the flight manual, and calculate the position using the stations listed there. If the calculated cg is within limits, you are compliant. That is what a government examiner will do, of course. That is what was flown in flight test, too, I am sure.
Hypothetical slouching pilots, seat removals and cross checking, and the like are working the problem to a very fine scale, and probably not what the manufacturer did when he flew the points and published the data, and probably not what the FAA did when they checked the manufacturer's data. It is possible that your personal method will introduce an error that could cause you to be out of CG, because you did not follow the conventions that everybody before you followed, thus making you the non-compliant exception!