Greetings,
It is my understanding that you should use Vault. For some reason Tme Machine does not capture everything in Apeture (metadata may be one of those things). Apreture being an Apple product, I am surprised that the Time Machine does not work flawlessly with Aperture.
In the book, Apple Aperture 2: A workflow guide for digital photographers (Digital Workflow), it states not to use Time Machine and use Vaults. I dont have the book in font of me, but it does give the reasons why. Let me know if you want me to look that up later on.
Mark
Canon 7D, Canon 10-22, Canon 24-70 2.8L. Canon 100 macro 2.8 IS L, Canon 70-200 2.8 IS L, Canon flash 580EX II, Canon xti