The system module is a prebuilt module that holds a lot of standard functionality in your application. Things like timezone, languages, user roles, sessions, and many more functions refer to the domain model in this module.
The system module is set to be non-editable but you are able to add associations or set generalizations to these tables.
For example, if you wanted to set up a table to upload files too, you can create an entity with a generalization to the file document table, and now either generate a document or upload a document to this entity. You wouldn't directly use the file document table, because you arent able to control the security for this table.
The same thing is set up in the administration module for the Accounts table.