Thanks for the quick reponse guys! I'm glad you can reproduce the problem.
I agree that, on it's own, a pixel with 0 alpha is the same as any other 0 alpha pixel, regardless of its RGB components.
However, consider a 2 x 1 pixel image where the left pixel is opaque white and the right pixel is transparent white. If you resize this image to 1 x 1 pixels, the resulting pixel should be something like:
RGBA = 255, 255, 255, 128
Now, if the right hand pixel had been transparent black instead, the pixel colour after resize should be:
RGBA = 128, 128, 128, 128
These two are obviously visibily different.
This effect may also occur when combining layers, but only with positive values of alpha.