To make the files renderable fast, I just removed all hair from both scenes.

The Mix node just always includes the alpha of the first image - this is so for a very long time.
On our todo is to make an option to ignore the alphas (mix them too, or add a 'cross' filter or so).

If you want to make a cross between 2 scene renders, you might better do this in post process - after rendering, via sequencer or so.