I am currently developing a plugin that is a combination of the Webtool plugin and the Navigation plugin. I make this for my needs and maybe someone will find it also helpful. I hope the first version will be ready in a few weeks.
As of right now, you would need to add an entity to a navigation in order to get the “nested structure” URL alias. But I have an idea how I could implement a generel nested structure for all entities into the plugin.