It does create a wealth of problems if you look at it closely. I'm more thinking that the people who threw in that connection/reference to VII didn't really think about the implications. I think they just figured it would be something fun to throw in there.

To further the issues (and also to extend the distance between X-2 and VII), I think it was said that it was Shinra's ancestors that even figured out how to harness Farplane energy. Shinra had the idea, but he didn't figure out how to do it. I could be making all that up though.

I will say it is stuff like this that makes me think that there should never be a remake of VII. I don't have any real nostalgic connection to VII, but I do think if that if they remade it, they would start tinkering with stuff and fans wouldn't be pleased.