Wow... it is always sad to see a project git hit by a C&D
I dont believe there is any doubt about who-dunnit, SE have a knack of dishing these things with no remorse, simply because they can afford to back-up their lawsuits whilst most victims cannot, even if they are legimatly in the right.
I dont know what that projects were about, but it looked to me as though the Modding was getting out of hand, when SE (or whoever reported them) didn't want the projects to be mis-interpreted in anyway, considering that it was still using their "engine".
IIRC the Chrono games were created by the legendary team of developers, almost all of whom are now working for various different companies.
So unlike SE's current games and IPs, they probably take the Chrono series far more seriously because of the additional strings attached to other companies.
IMO it is just SE's way of trying to keep their friendliness with those other companies more than an attempt to protect the IP.