The other reason that the Alpha channel is more effective than the transparency channel for layered materials is that you can boost the Alpha channel intensity beyond 100% (which is 0 on the Vue Alpha Boost Slider).  In some cases, I have used procedural noises to generate the Alpha for a particular layer.  Boosting the Alpha Value beyond 0 will intensify the coverage of the layer without having to adjust the alpha map or alpha noise.   The point is moot if you only want to restrict the Alpha intensity to values of 0 or below - in which case Alpha and Transparency are identical