This is typically used directly for special page navigation and history navigation.
It is also used to calculate the maximum allowed value when the user manually specifies how the list is sized. Manual sizing can often be done by manipulating the list URL even if the form does not provide a means to do so. Having a maximum limit regardless of the means of input helps prevent abuse.
Aside from the Area-related navigation you mentioned, the other Navigation settings are used depending on the specific context the list is in (such as if the article is part of a book). If you only ever use area-context lists, then the other settings may rarely apply to you.
Even for the area-related navigation you mentioned, which only sets the default area list size, "Items-per-page choices" is still relevant per my point about maximum allowed values.