Ah ok, now I understand your questions. No, the problem with A6 shaders on geometry had nothing to do with the BSP tree.

A6 rendered blocks one polygon at a time. This became pretty slow when you used surface shaders. A7 renders blocks together as a whole mesh, which is a faster method especially with large blocks or when using shaders. That's why it was not recommended to use shaders on geometry with A6, but is no problem with A7. The BSP/PVS algorithm is unrelated to that. It only determines which blocks or entities are rendered in a particular view.

The access to the second UV set is the same in A6 and A7. It's described in the shader chapter.