One flat seems simpler and less prone to having things get out of sync
(particularly when dependencies aren't specific to an exact version number).

Isn't this handled currently using Ivy's resolver / mechanism now anyway?
Maybe I'm missing something – could you elaborate?

This issue is obsolete. Until 0.5 we saved the Gradle dependencies in svn. The issue was about if we should organize the dependencies in folders. Now we get the dependencies from remote repositories.They are not stored in svn any longer.