The following articles describe how fly rods are manufactured.

http://www.itinerantangler.com/podca..._rods_are.html

http://midcurrent.com/gear/how-fly-rods-are-made/

You mentioned material quality including the rod components and graphite flag as differences.

The main design components for the rod blank is the design of the mandrel and the shape of the flag. It is natural to assume the mandrel tapers from top to bottom with a consistent taper. One assumes that the taper of the hollow inside of the fly rod is consistent. That is NOT necessarily true. The outside taper of a fly rod may be different than the inside taper because of the shape of the main flag.

Fly rodders also assume that the graphite pre-preg cloth that is used for a fly rod is the same for each section of the fly rod. That is also NOT necessarily true. The designer chooses the pre-preg and different composites can be used for each section.

After the rod blank is baked and cured, it is released from the mandrel. After the cellophane tape is removed from the rod blank, spiral ridges of pre-preg resin remain on the rod blank and these must be sanded off. Almost all of the major rod manufacturers MACHINE SAND the rod blanks. Some high end rod builders like Burkheimer hand sand the blanks. Variation in how much material is removed form the blank can cause the rod blank to vary as much line wt.

I know that Jason Borger designed the mandrel and specified different graphite composites for different sections of his latest fly rod produced by Burkheimer.