We have used photoshop for our compositing and post processing for many years, and dont really have any issues. Although recently we are looking to use After Effects for compositing the passes. The main issue with photoshop is that it doesnt support floating point images (16bit), where was After Effects does.
We render all our images as passes, and you are correct, it does give you so much flexibility. Changes to materials, lighting, etc can sometimes be a very simple tweek in post production, rather than wasting time rerendering your scene again.
The Gnomon DVDs are a great place to start, even if you dont use the exact same software. I have watched the compositing in Fusion, and a lot of the work-flows, and understanding, can be used in most applications.
As for the pre-multiplied issue, there are several ways around this, but if you want to do things correctly, use a compositing program like Fusion, Nuke or AE. I think Fusion also has a free learning edition too.
Hope that helps, Deano!