Does anyone know if VP is supposed to maintain the layer's original transparency?
Nope. Since it creates a 3D layer, it has no concept of these things. It merely cares about the diffuse color and distorts them to fit on the virtual plane. The texture resolution is defined by the document resolution, but the process of baking the projection always results in some loss of sharpness. It's no different than when you would use the free transfrom and warp tools in PS to do the same. Alignment issues have been discussed. The gist of it is, that you PS doc must match what comp size you later use in AE, as VP doesn't create neutral 3D data, but ratehr merely aligns relative to the doc. Of course this kinda works against the first suggestions, so you have to find a suitable compromise. You will not be able to avoid funky values at all cost, though. sometimes they will be tiny, sometimes they will be excessively large...
Thanks for the reply! It should be easy for Adobe to fix this transparency issue, though. I'll have to file a feature request. If it just treated a layer's transparency as an alpha and treated the rgb as straight, then the png it saves out for each plane could just be rgba. Seems simple to me!
You can, however, edit the individual png files that photoshop creates as part of the vpe expor - ie delete the white bits.
Because the extra bits are solid sections of white it isn't too hard to do and the vpe still reads it as desired provided you don't change the png file name when saving.
hope that helps!