Getting Transparency to work correctly with baked PNG and single mesh made from blender

I have joined all of my parts to a character into one mesh and baked one texture in blender. When I tick the alpha box to make the texture alpha appear it looks good in Blender and retains all of the gradient alpha for smooth and clean transparency.

I export an FBX file, externalize the material for editing, and set the PNG texture to import the transparency. The preview shows transparency correctly on the checkered background. What I end up getting is where there should be transparency, there is a lot of mess like the UV is wonky. Cutout works but since it clamps/ignores the gradient of the alpha, it makes hard contrasting lines and I loose partial transparency. Am I SOL and need to make characters without transparency, or am I simply doing something wrong? I know this works in other games made with unity so maybe I need to write a new shader for it?

There is this image just incase...

 

Still not working. I may have to change my question to what commands do I use when writing a shader to get smooth alpha transparency?

 

did you try rendering mode Transparent in the material? (screenshot shows only Cutout and Opaque modes used)

 

Yes, dunno why I forgot to mention that, and it has a strange effect like the Z order gets inverted.

 

oh i see (looks like alpha sorting issues).
but you want only the eyes to be transparent right? can use different 2 materials then.

 

Ah, ok. Yes, eyes and eybrows and eventually clothing. That sounds familiar from reading about Unities draw cycle long ago, and I must have derped the memory. I tried making another Material for the things I need transparency for, one for each so they don't fight each other, I think this works but instead of using Transparent it seems I have to use the Fade mode instead or the outline of the mesh still faintly shows. I was kind of hoping to not have to use too many materials, but it's probably ok as long as they are all on the same mesh. Thanks for the help!

 

I don't know if this can help you, but what works for me is this. I did 2 bake textures, 1 the regular bake texture, and the other is just a glossy bake type, only the color and that created a B&W image that then you can use as a mask in photoshop...