I can't answer for any other frameworks, but the quick and dirty of it is this: The packaged versions have namespacing to protect your global namespace from pollution, and of course dealing with load order correctly, since packages get loaded before your project does. As for bootstrap in particular, the atmsphere packages override CSS locations to make everything 'just work', especially with glyphIcons.
Of course there are other benefits to packaged versions, including specifying what components run on the client versus the server, what that package relies on to work (For instance underscore), what version of Meteor the code is compatible with, possible github repos to make sure you get the latest version whenever you do a meteor update
and more. Meteor has put a lot of thought behind the packaging, so it's worth using packaged versions.