Okay, thanks, I finally got it!
But have it really to be necessary to define two materials in C4D for that effect? Or could you perhaps change the blend material (the material helper tag) in a way, to get all the needed informations out of one C4D material where in the color channel is one of the textures defined and in the alpha channel is the texture with the alpha informations associated.
And what really would be great, if even the material conversion feature of cindigo would be able to handle C4D Materials with an alpha map automatically correct and would create the material helper tag with the right blend material settings.
By the way, what do you think about a check, if materials are still converted when the cindigo convert materials fearture is called?
I made a few tests and here are the results: