But there is any specific reasons of why they are "transmitting money" in the document? Can't read it all now.
No, there is no specific allegation in the document, just a general admonishment against violating the statute. California clearly has their wires crossed because, even under the most expansive interpretation of the law, the foundation is not a money transmitter.
They cannot be a money transmitter simply for advocating for Bitcoin as there are first amendment issues preventing regulation of that type of speech.
If the definition "facilitating the the transfer of money domestically or internationally outside of the conventional financial institutions system" is sufficient for them to build a case, then I think this is a serious challenge. Funding the infrastructure and developing the code-base has to meet a definition of "facilitating" I would have thought.