One
example is when the puppet mesh generated by the alpha does not have to change,
I may for example just have made sure to keep the new PSD version layers within
that puppet mesh, so all I want to do is swap all layers in a comp at the same
time rather than one by one.
I like the puppet tool but I wouldn't want to trust it when swapping the layer sources.
Have you tried Duik? It's free and awesome. I haven't used it for a few years and can only assume it keeps getting better. The results are slightly different to the puppet tool - no smooth deformations - but it is much easier to swap elements in and out:
Worth a look.
-Chris |