Page modules are the first choice for apps that want to add a whole page in Jira. generalPages module can be used to add a page that will be accessible from the main Jira navigation. However, in order to add a page accessible within project navigation, it is only possible with a Web Item, where app's content is provided as a Web Panel.
As it turns out, the properties available for Web Panels are limited comparing to what is available on generalPages, therefore apps cannot provide the same user experience within project navigation as they could in the main navigation (refer to ACJIRA-1207 for example).
Ideally, Jira should support Page module in project navigation, in order to increase adoption of project-centric model by apps, without negative impact on end user experience.