Somewhat confused about URL Helper

Regarding the URL Helper functions, why is the "CI master-file" (index.php) often included in the output?

Probably you already know, but the answer is:
by default, CI outputs index.php in the URLs, because it works without mod_rewrite or rewriting the URL.

But in most cases, we do not use such URLs, and we use rewriting and set Config\App::$indexPage to empty string.

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