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To say assigning issues to projects allows management of a project's backlog is valid I think. For people who have lots of projects, it's useful to keep them categorized as such.
The tree hierarchy of projects can be very useful in keeping things organized. For example, in the projects I work with, there are several high-level groups of projects, and then some additional sub-group of projects is in the tree. The leaf project nodes make up the actual specific projects. The hierarchical grouping allows the issues associated with those projects to be quickly selected by viewing the desired level in the tree.
When planning iterations, it's simple enough to identify the high-priority projects and then assign their issues to an iteration based on the backlog of issues in the projects.