I don't think it's a contradiction at all. She's the only one who has understood Cloud, and this was proven throughout the compilation. She's overcome so many struggles with him, expressed so many feelings... knew the right things to say to him, and devoted her very being to him. Of course she's the one that connects with him best, which is why he opened his heart to her, and to her only. The quote says that she "still does not understand some" of the complexities of Cloud's heart. You can't expect her to know everything about him, she's not perfect. =) Besides, her not understanding a few things doesn't mean that she is magically not connected to him anymore. There will always be a few things you don't understand about someone... but it doesn't hinder anything, or change the fact that she is the woman that can get into Cloud's mind and heart, and effect it to a great degree.