Guess my observations have been a little different. Whenever I've been lucky enough to find a car with mostly original sheet metal, the fit of the body has been excellent.
I have a March '65 San Jose convertible I'm working on now, it has original quarters and I believe the quarter extensions are original, they are the non-gasket type with the LH cast: C4ZB-6528073-A and the RH: C4ZB-6528072-A.
I also have a Jan '66 Metuchen GT fastback that I will be assembling soon, the quarter extensions from that car are the gasket type, LH cast:C5ZB-6528073-B and the RH: C5ZB-6528072-B.
The single year '65 and '66 MPC's call out the same number for all cars, C5ZZ-6527703-A and C5ZZ-6527702-A. Interestingly, the '75 version has the same information, no differentiation between 65 & 66. Guess it was a crap-shoot what you might get in one of those boxes... depending on when it was packaged. I would imagine most anything in a Ford oval box would be the gasket-style extension.
I suppose it's possible there were only 2 common types of extensions. If anyone has any extensions with differing engineering numbers, please share.
Edit: I have an NOS red-oxide RH 65-66 convertible quarter panel in the garage, mint with paper covering still on it. I put the C4 and C5 extensions up to it. The C4 extension did not go all the way to the inner edge (that would be parallel to trunk lid), was short maybe 1/8". The C5 extension fit perfectly. I also put the C5 extension on the SJ convertible I mentioned previously. The extension fit was too far off the inner edge, pretty much the opposite of how the C4 fit on the service quarter panel.
I'm sure there might have been variances in the quarter panels that Ford serviced, but this could be something to consider when there is a problem with quarter extension fit.