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When friendly aliases are used, the URL would look like "...site.com/alias.html". If you use index.php, it looks like "...site.com/index.php?id=42" - using the ID of the resource being requested.
The rewrite rules change the "alias.html" to "index.php?q=alias.html". MODx then uses the "q=alias.html" part to look up which resource has the alias "alias", and takes it from there.