What is the reason behind the current menu structuring
You can create as many menu items as you want and have them point wherever you want. You can do this in code and in the UI.

Drupal menus have plenty of flexibility, especially with contrib.

More:

You can set up many different menus (and not just one overall hierarchy) because that way you can have more than one menu. You can put them wherever you want on the page. You can have a sidebar menu and a top-strip menu and whatever else.

Internally, the menu system is really a routing system. Drupal uses the same set of code for routing requests as it does for presenting menus in web pages. Each route/item can have its own permissions, so the list of items the user sees is determined by their role, automatically.

In short, to recap: The reasoning behind Drupal menu structuring is that it's flexible.