I'm not sure you really understood what I was saying. I'm not suggesting adding more rows to the palette, just using some of the existing rows for "blended" colours. Rows 10-11 for example can be directly edited within ZQ. They're usually used as additional sprite palettes, but if you're sticking with just csets 6-9 for your sprites then you've got 16 free colour slots going unused in just those two rows.
Now correct me if I'm wrong, but ZC handles transparency by scanning the 256 colour palette and finding the colour that's closest to a 50/50 blend of the "upper" and "lower" colours (assuming it builds the colour table with 128 for the rgb values), yeah? If so, then you should be able to manually calculate the "perfect" blend of any two colours, and if that blend colour exists in the palette it'll be displayed whenever those two colours are blended.
As an example, let's say you're working in the classic set (fewer colours, makes it easier) and you make some solid black shadows for a transparent layer 6. You want Link to look perfect when he's under the shadow (no weird colours or anything), so you take Link's three colour values and average them with the black shadow, giving you a dark green, a dark tan and a dark brown. Take these colours and stick them into cset 10, which isn't being used (though it could also be) but is still part of the 256 colour palette. Now when ZC scans the palette for the most appropriate colours whenever Link's under the shadow it finds these three "perfect" fits in cset 10 and uses them rather than some "close enough" grey or whatever.
The classic tileset has so much empty palette space it'd be trivial to set up two, three, maybe even four "blend maps". For most other sets just finding the space for one would be hard enough, and I can't imagine having any more than two unless you really optimise things.