Mattias,
Are you saying that if you make a Clipping Mask, in the PNG the parts clipped (away) are white or something instead of transparent, or are we talking about an Opacity Mask using grey to get partlal transparency/reduced opacity?
In the former case I believe the parts clipped (away) should indeed become transparent in the PNG, but in the latter case I believe you can copy the knockout path (Group) and give the copy the desired appearance (colour and degree of transparency/opacity) then select the original and the background to knockout from and Pathfinder>Minus front as suggested by John; or you can turn the original black and select it with the background and make an Opacity Mask thereby keeping everything reversible.