What Exr is doing is applying the A into the image and not making it editable...althought the transparency is applied, the transparency is effectively "lost" because it cannot be got at.
Another point that you might not be aware of is that the RGB data is built from the RGB of the object against the background. The background might often contributes nothing to the alpha, but does to the RGB... so when the alpha removes the area it removes RGB data. Obviously this is exagerated when using pre-multiplied values of not 0 or 255, because it removes a proportion of the RGB (including the background) related to the A value.
Because of the way PS can't handle pm, it is the exact reason why it shouldn't assume alpha isn't transparency.
If I render an object with no transparency with the values 128,128,128 and A=0 then render it with 50% opacity, the image is 128,128,128 and A=128. The problem is that although the pixel values are stil 128 in the RGB, the image is transparent! You can't get that "solid" 128 RGB data out because PS ties it's transparency in with it... you can't unhook the two apart from each other. There's no layer mask to lose, or alpha, it's 'baked' the transparency into the image...
It's not so much that the transparency is lost, it's that the image is irrevocably broken... I can re-generate an alpha from the transparency... i can't see how i get those pixels back to full opacity though.
perhaps there is a way of doing it... how do I get a that image back solid? The pixel values haven't changed, they're still 128, 128,128... the alpha is gone, there is no layer mask, the layer is 100% opaque... yet there is a transparency value attached to each pixel that I can't get at.
The only way I know how is to put the exact colour in the background that was used in the renderer... but it might not be a colour used as the background, it might be an image... it might be a background plate which normally carry no alpha contribution... that's the problem.
You don't arbitrarily apply transparency in 8 or 16 bit to other formats before they are opened... why do it in 32 all of a sudden? They all support transparency once in PS (well its PS that supports it, not the format)... same as Exr.
In fact, it was this exact problem that prompted the backstep on alpha. I can't see why you can't see this as the same thing, because from our end it is.
If you want Chris, I can send you the exact files. A simple transparent box floating over a background, rendered. Normal alpha generated from the opacity straight from the file. All standard stuff, straight from a standard renderer. Your challenge is to tell me what was in the background. Your 2nd one will be to re-create it. With the CS2 you can... with CS3 you can't.
But does this mean we can load the CS3 non extended plugin in, or does the app do the damage? Could that be perhaps made available if it solves the problem?