Transparency or Alpha Channel for Cinema 4D Materials?

Is it better to use the alpha channel or the transparency channel in a Cinema 4D material? Does it matter if the texture for the alpha or transparency is 8 bit or 32 bit?

As no materials from external programs are imported (FBX does not support this), it doesn't really matter. As Unity's transparency shaders use the alpha channel of the base texture for transparency settings you probably should set up your materials in Cinema this way, so you don't have to change your textures once in Unity.

So, the answer: use a regular texture with 8-bit alpha channel (and 8 bits per color channel - format ARGB32) for transparency inside Unity, as this is the way the shaders want to get it.