I would go ahead and report this to the Bugs forum and see if the IM folks can figure out what is going on. Provide a link back to here for examples and a short explanation of the problem.
I think the real question here is where is the white coming from - PS or IM. What determines the background color for pure (background) transparency. That color seems to be getting mixed with your antialiased drawings even without transparency overlays or gets mixes with the color of your items when doing transparency blending. Why is white and not black or any other color? Is that defined in PS or set when IM reads the file?
I created a pure transparent image in PS and saved it as PSD. Then let IM disable the transparency and got a pure white image? So is this white already there in the PSD image or is IM adding it?
Two other non-IM imaging tools that I have both show white for the background under the transparency. So it would appear that it is in the PS file in some way. How PS deals with it is not clear to me. I do not see any way to set that background color under the transparency to something other than white.