The transparency does work, and you could bake it with the method I showed. The reason it would not work perfectly is simply because the alpha is not cut sharply. There are artefacts even apart from the wings. Look how I increased the Greater Then, the bigger the “alpha holes” became.
It should be corrected in a photo editor like GIMP or PS, if you want a cleaner image. BUT you may try using the compare node as well. You may need to flip this around, but you can see it does a pretty good job, measuring the BW polarities, taking the supposed alpha into account, where it should be. As you increase the Epsilon, the alpha tightens up.
Here you see 2 picture. The first one is when i try “Emit” and the second one is when i try “Combined” and as you can see i have blend mode “Alpha Blend” and i have Math Greater Than but as you can see it is still black below the UV Unwrap. The holes in the skin is still black. And yeah, i know about the artifacts. Thats not a problem really. But it should not make all bind the UV Unwrap to become solid black color.
It works perfectly for me, on its own as well, and playing with the Greater than only, you can cut the mistakes of the alpha cut, then bake it with Emit simply. This way you can reach a nicer alpha than the original one. Yet, it will not be semi-transparent in some places, but you can also sort it out a bit differently, maybe with some other math nodes… If you only want full transparency, this method is fine.
The real problem is that blender (anymore or whatever) doesn’t give transparency rendering but not in in baking (even if you seee it inshading ). Anyway the OP is using an image and wanna reback it to use as a texture. So i would suggest to do two bakes and one compositing.
First: back the as you did (or just use a diffuse shader) and save the image.
Second: use alpha as emission (maybe also just a emmission shader) and back from emmison and with margin 0px (!!!)
Third: use composition to make a new texture image with color from first and alpha (but from color !!!) from second and the correct dimension (here 1024x1024).
Wow… Could you show some screenshots on how you did this or do you know any tutorial for this? Anyway i was able to find out how i used to do it. I used to just use the “Clone Brush” in Texture Paint to clone the texture from the first on to a new transparent texture. But that takes time. It would be a lot easier if i could use the composition to make transparency