Got the chance to make some screenshots.
This is the actual best result from the original snes9x (dithering is 100% correct and does not affect any other game)
This is with the stock method (forced to absolute pixels 256) - As you can see the transparency effect is gone
This is with gdapt. The error prevention level is highest so that other games like Link to the Past are not affected (font issue). Now it is a mixture of the dithering pattern and the transparency.
I would like to get the result from snes9x. But I have no clue anymore. Kirby should have the transparency. But games like Link to the past or secret of mana should not be affected (font or art chessboard in SoM) Maybe someone has a clue.