Hi Ralph! Thanks for the welcome.
I just discovered Sitepoint today -- there's a lot here and I'm looking forward to engaging some of the forums.
The method you mention is definitely the ideal situation. I'm a front-end developer and am often handed mockups from designers who have use blending modes on layers. For instance, a white to black gradient blended with darken to simulate a transparent to black gradient. Up to this point, I have always had to just flatten the image to use the effects, or try to redo it with a transparent gradient manually.
Increasingly I'm building these designs into WordPress themes where I'm allowing users to set background colors from within the theme settings. This means that all of my image-based shadows need to be completely without color, just black/gray to transparent gradients. Basically, alpha channel only.
From a technical aspect, I would need software to look at a blended layer and the layer over which it is transposed .
Next, it would need to use some a pattern to simulate the "luminosity" of each blended pixel -- i.e. take the rgb values observed in the flattened image and pick a shade of gray that it roughly matches. It would have to calculate that shade of gray using rgba(0,0,0, x) where x is equal to the opacity over a white background.
But what happens when you've taken a shadow that was designed on a light yellow background, and want to place it over a dark blue background, and still get a shadow effect (not a glow)? To work around situations where the darkest pixel value of a shadow gradient is lighter than a chosen background color we could do the following: If all of the pixel values in the shadow gradient were shifted so the darkest pixel value was always adjusted to rgba(0,0,0,1), then you could re-adjust opacity later in CSS to make it look "good" over any particular background.
Just some thoughts. I don't think there is any way to currently pull this off in an image editor.