Are setting the color to transparent to hide images?
That's also not efficient since the GPU is still expending cycles to draw all those transparent pixels.
That also won't work on the shadows with the Skeleton shader.
It doesn't account for vertex alphas, since shadows use hard alphas anyway.
I'm not sure what the semitransparent rectangles are all about.
Does your scene have fog? I remember we disabled fog in the Skeleton shader a few updates ago. SkeletonLit might still have it though. In that case, it'll be disabled it.
Neither are supposed to work with fog at all since they're premultiply-alpha shaders, and both are supposed to be barebones.
Thanks for reporting!
You can change all this behavior by editing the shader code, or making your own.