In the SharePoint the site structure and features has hierarchy
It can consume all the service applications and has it`s own features can differ from the other web application
A web application can contain more than one site collections which we can activate the different features based on usage but all the site collection consumes the web application features.
A site collection can contain more than one site and site features can be maintained differently from another site. But all the sites can consume the parent site collection and web application features.
If you want to create sites with same structure and features you can create them as a template and new sites can be created from your custom template.