The project files are put where FCP X wants to put them. If you render anything, it puts the rendering where it wants to put it.
FCP X has three opportunities to lose something - it can't find your project, it can't find the event, the event can't find the media. We see it on this forum all the time and right now 10.1 is managing all that and screwing it up for some people. We see FCP X updating events and projects...
With Motion 5, I put my project file where I want - in a folder for that project. In that same folder, I have all my media. It's not necessary to have a feature where it moves my files for me to another drive, etc. I simply drag that folder anywhere I want and all the links are in tact because the links are relative.
With FCP X, even if I don't copy the media to the events folder and leave it where I want, it still creates a folder with its own hierarchy - Backups, Old Versions, Original Media, Render Files, Transcoded Media...
FCP X's method opens people up to more problems, obviously. You don't see people on the Motion forum talking about how Motion moved media or put it in the trash etc. The only thing that can happen is the small XML project file can't find the media and so you simply relink and you can use Spotlight for that.
Seems like there are more headaches with FCP X's method.