The shuffle Node is for mixing RGBA channels, you can have only one input (A) and reorder it like BAGR instead of RGBA
or mixing two image's channels , like take R and G channel from input A, and B and A channels from input B...
For adding an alpha channel, I think you can setup it in the read node, or if you put a shuffle node after the read, if you have access to RGBA channels, then set A channel to 1
I haven't natron at hand so I can"t do further tests, if you've got issue I'll take a closer look at it !
Happing natronisation !