Alpha channels

I don't think so, the reduction should only affect a compiled XCode project. Just test it and import your gfx into a new Windows project.

You can change the iOS properties of specific objects to ignore the global color reduction setting. It's good to have it enabled for your entire app, but with things like gradients it really destroys the smoothness so it's probably best to turn it off on those objects.

It is the color compression setting.
As RhysD sais you should always leave it enabled globally and only disable it for individual objects where it gives otherwise gives bad results.
If you load a PNG at runtime it uses the full quality 32bit color format though.

Color reduction works by squeezing the color information from 4 bytes into only 2 bytes.
Normally it spends 8 bits on each color channel (Red, Green, Blue and Alpha).
In color compression mode with an alpha channel it can only spend 4 bits on each color. That gives you 16 different levels of transparency instead of 256 which is a big difference.

For images where there is only a transparent color it uses a color format where it uses 5 bits on each color and 1 bit on the transparency (invisible pixel or opaque).
That gives you 32 different shades of each color channel you can mix.

If the image is completely opaque (has no transparent pixels at all) it uses 5 bits on red, 6 bits on green and 5 bits on blue.
It does this because the human eye can see more shades of green than the other colors.