How can I remove Features modules from a site without affecting functionality?
When you are absolutely sure there is no custom code in the feature module you can safely recreate the feature by going to /admin/structure/features and then change permissions and/or disable modules such as the Overlay module that are declared as a dependency in the feature.

You can recreate the feature and remove the unwanted components:


Go to /admin/structure/features
Click the 'Recreate' button next to the feature
Uncheck all dependencies or other components that you don't want in the Feature.
Click the 'Download feature' button.
Replace the Feature module in your modules folder.


When you are not sure there is any custom code in the feature module do this on a local environment and check all changed code via Git to make sure only the components you deselected are removed from the feature module.