http://hastebin.com/bujarihenu.sm

Sorry this is the source (other had vertex RGB linked, not alpha):

http://hastebin.com/pevifunose.sm

Note that this is on an unlit shader, if that makes any difference

Edit: tried this on Lit, Phong etc. and on different outputs. The texture alpha channel is displayed in the shader editor, but not in the engine.

Yep the texture alpha and the vertex alpha channel definitely have info there, but the problem is with using the texture alpha channel with the vertex alpha channel - Multiplying by R,G or B works, just not the texture's alpha channel for some reason. Also, when you hook the vertex alpha Texture Alpha up to the emission on it's own, it fails to display it - possibly the root of the issue?