The node and menu commands and the chapter structuring commands are independent of each other:
You can use node pointers and menus to structure an Info file any way you want; and you can write a Texinfo file so that its Info output has a different structure than its printed output. However, most Texinfo files are written such that the structure for the Info output corresponds to the structure for the printed output. It is not convenient to do otherwise.
Generally, printed output is structured in a tree-like hierarchy in which the chapters are the major limbs from which the sections branch out. Similarly, node pointers and menus are organized to create a matching structure in the Info output.