Regarding the features module: I am working with a module which was created by features. I see a lot of .inc files in the module, but see very few actually included. Does this make any sense? I know that they are all being used and are creating fields etc.
Most include files exported by features are included on-demand by the modules that define that type of component. For instance,
example.views_default.inc is included by the views module when loading default views. This is a common pattern in Drupal, not something that is specific to Features.