Jim,
The shift linkage is not bad if it is all working properly. However parts wear out and problems can result. I had shifting issues in bot Sat and Sunday races due to a loose bolt in the back. I need to be able to mod the system to make sure it does not become a problem again. Now a Mod can be something as simpy as drilling the set scre for a lock wire. It could also be replacing the set screw in a hole to one where you actually bolt in to the hole with threads. Same goes for the pin joint at the shifter. Sometimes you can reaplace the shifter. Sometimes the black rod is worn out too and that is harder to replace. So it makes sense to allow you to replace that joint with something more robust.
Currently there are no "kits" out there that do this other than "short shift kits" Short shift kits intent to reduce he shift throw in an effort to make it faster. Now I don't know how much it helps, but it might be a performance edge to shift faster than stock. However it is maintainabily repair to mod things to ensure you don't miss a shift or miss a gear.
So the current rules allow to mod the shift linkage, but not shorten the throw.