I'm preparing to re-model a Table Mat (like a Tatami Mat) tomorrow. I will need to do some baking from geometry onto a plane-texture. I know how to do that, except I don't know how to bake the alpha? I don't see alpha in the list of what I can bake in Cycles. There is transmission, but I think it's not the same. Is there a way to bake alpha? I'm pretty sure I will need it to compose materials in the Compositor. Would it help if I set world color to transparent in the Film tab in the Render properties? Will it then bake with transparent alpha?
I don't think it's possible to bake alpha directly, but you can try making a new shader mixing a white and a black emit shader together using the alpha of your textures as mask, then bake that into a new texture.
It will be a bit tedious if your scene is too complex, but I don't know of any other way. If you have too many objects it's probably a good idea to try to automate that using python.
For cycles what I did was bake 2 times creating 2 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...
I'm not sure what you need but I believe you should be fine just baking the textures and use it as diffuse while using another texture with alpha information on the same material to provide the transparent areas.