Square-Enix is a solid and well-established corporation and will listen to any new venture that can benefit them and the gaming community. They may not be officially prepared to accept a project or request of publication that is as serious, well-adapted, and comprehensive as this, at least not one coming directly from the fan base. Players of RPG's always want something more, whether that be a good sequel or something totally different like a novel or a movie. In many cases, they want them all, so why not benefit everyone and provide them? Obviously, as we have seen with the creation of a Final Fantasy movie, we know that an exception can be made somewhere down the line by an individual who has a mind open enough to understand this and to act upon it. This movie, however, was an extremely costly venture for the company that it may not want to repeat without more promise of success. A novel, however, is considerably lower in risk and cost.
For reasons also mentioned in the "mission" section above, this novel can only benefit Square. It's a product that will be ready for them, reducing their work to a minimum. It is also my understanding that the novel must pass their standards, and I will work with them to make sure that any concerns, inconsistencies, and requested changes that they may bring up are addressed. Publishing the novel exposes the story of Chrono Trigger to the mainstream public (especially with the proper marketing and distribution) in a new and sophisticated way, opening the door to new opportunities and potentials. Not only could new interest spring up for role-playing games, but a successful novel could very possibly lead to new ventures, even including a movie, a Chrono Trigger remake, or a new game in the series.
In light of this, Square USA, as I have seen in the past (note that this was before Square Co. and Enix merged), is completely powerless to take a decision such as this completely under their wing. Though they are the quickest and easiest outlet for a project born and created in the USA, the true origins of the story and its game go to the country of Japan, where the main headquarters of Square-Enix reside. While the American office may be able to act as a liaison to the main headquarters, it is there in Japan that this novel will have to be presented to the officials who will evaluate the opportunities for corporate benefit represented in the cause of the Chrono Trigger novel.
There, the corporation of Square-Enix must realize that the acceptance of this novel is only beneficial to everyone.