No, Creation of all Things is NOT omnipotence. That is just a common misinterpretation.
If it were that way, then all this would not be happening, for the Rikudō Sennin would only need to imagine Ninshu working and thus not distorting into Ninjutsu.
No. He created Ninshuu, but not via Banbutsu Sōzō. Banbutsu Sōzō is just the most advanced Shape and Element Manipulation, so it can only create things with extension.
Ninshuu is both a skill and a phylosophy (does not have extension), therefore it cannot be created with Banbutsu Sōzō.
One of the following days I will make a thread about the Chakra, the Yin-Yang, the Natural Energy... And it will also involve Banbutsu Sōzō. So I think that you might be interested.