I've just updated these documents to reflect changes in the new 2.3.6.4 release.
Configuring Initial Content
Populating Feature Content
modules are not shown in the menu pages are shown in the menu and modules are hosted in pages. It is not currently possible to set the include in menu setting for pages, but I will implement that for the next release. It is possible currently to set page view and edit permissions but not module view and edit permissions, I will also implement that for the next release.
Best,
Joe