~/.../TextMate/Bundles only contains the changes from ~/.../Pristine Copy/Bundles _if_ there is a bundle in the Pristine Copy folder.
Well, or if there is a bundle inside the app itself.
This whole mechanism, though, is somewhat outmoded, since if you're going to make changes you are just as likely to make them in some script inside the bundle's Support folder - and that, of course, does not get diff'ed into TextMate/Bundles.
m.