Sheff, I know what you are saying and I agree it would be nice if the user could specify how they'd like the transparency tool to do this. In a similar vein, I have long wished, when doing linear, circular, and ellipical fills that they would start from the Flat-fill color and end in white when dragging or when applying to an existing Flat-filled object. This would be similar to how the transparency tools currently work.

If we couldn't set and save this in Options, having a "Reverse" button in the Standard bar or the Info Bar for the Fill Tool and Transparency (similar to the Reverse Path button found in the Shape Editor Info bar) would be a nice alternative.