I'm a little confused now. It's pretty easy to swap the read and blue values in a vertex shader. What has this to do with the input registers?

The v3 and v4 registers pass the diffuse and specular vertex colors to the shader. In T&L mode, vertices do not have any diffuse and specular colors. Those colors are calculated by the hardware from the material and the entity color and environment lights. So those registers are always zero in A6 mode. They are only used in A5 mode.