The Phantom in Spirit Trakcs is EXACTLY the same Phantom as from Phantom Hourglass, the Crawfish Shield is one of the shields used in the post-flood world - it reprisents the way things are in that time and all. They are using steam technology, this only gets created by the events of Phantom Hourglass and onwards.

And major fact- the Phantom in Spirit Tracks is a major part of the stroyline; the storyline is what influences timeline. The Phantom is one of the Phantoms from Phantom Hourglass, meaning Spirit Tracks comes after they were created: they were created by Bellum in Phantom Hourglass.

"Hyrule defend itself? HAHAHAHA!" I always crack up when I see that. xD