Harpo is correct. The "Old" textures (like from Original SotSE 1.0) use the CL, and DA texture different than "New" textures of Entrenchment 1.151, and Diplomacy 1.31. The normal maps (NM) have never been changed since the Original SotSE release.
The "Old" CL texture used its Alpha Channel for Specular Maps. The "New" CL texture uses its Alpha Channel for Team Color. So ever since the original release of Entrenchment, The CL textures alpha channel has been Team Color.
The "Old" DA texture used its Red Channel for Team Color. The "New" DA texture uses its Red Channel for Specular Maps. So ever since the original release of Entrenchment, The DA textures red channel has been for Specular Maps.
The shader swap was supposed to improve in game performance. However I never saw any performance improvement by swapping the shaders like this. The game ran the same as it did before. It did however simplify things a little more for the modders.