I'd think these are two very different functionalities for different usage.
Darken, even if it's just black, is very useful for shadows (replacement for the ugly dithered shadows)
Since they would be part of the graphic rather than created by the game like the plane shadow, I don't think they would cause any trouble in the drawing orders. If restricted to black, it would only take 3 special colors, possibly shades of gray close to the given percentages.
The way how to scale that in the game seems pretty clear to me. As far as I can see, special colors have the top priority, after that it's normal colors, darkest first. Lowest priority for transparency. Applying the same with inclusion of Darkened area. they would have lower priority than any color, most opaque first. Which means within those darken colors, 75%black would have highest priority, and 25%white the lowest. (Though white would not have any visual effect at all)
To create an antialiasing effect, darken is not too useful though - It works if the graphic you are using is dark already, or if the background behind it is very bright, but that's somewhat unreliable. You really need a blending effect to do that, even if that is more work and not good for performance.
Therefore I think it would be best to have both, possibly starting with black shadows since that's easier, but not under the pretext it could be used for anti-aliasing in trees.
I guess the real issue with blending is that it would be rather silly to use it for antialiasing if you are just going to zoom in and out the same way as you always did without implementing a similar blending for that. At least that would be my concern, just like the current dither-shadow gets really ugly really fast in anything but 100%Zoom, any zooming implementation for transparent blend pixels that follows the current logic is bound to be troublesome.
That being said, just as a disclaimer: Pak192.comic has black outlines anyway, any antialiasing we could possibly do is with black, where blending and darkening is the same thing. Therefore I might be biased since blending would just be used for semitransparent materials, like a glass roof over a station, but surely not for trees.