I didn't really follow the whole Legends 3 thing, but wasn't that Capcom? Since MML is Capcom's IP? How would it be his project, if it's Capcom's IP? You're confusing me here.
Try to focus, Capcom is a company, Inafune is a person, people create things for companies, these creations then became a company IP. You understood this part? Then lets continue...
Keiji created Mega Man (not alone, but still created it) and continued to do Mega Man games for Capcom. Okay until now its common knowledge.
If he is working in something (even more when he is creating something like story and gameplay), then it is his project, since he is working on it. Im not saying that he will own something that he creates, since its being made for Capcom, but it still his project, his work.
You understand what I mean now? Im not saying that it is his project as in "I won something and thus I can do anything with it", it is his project as in "I've been part of it, developed it and my ideas were in there". Companies do that, hire people to do their work, even have ideas for them.