Sure, the DevTools allow you to investigate the shadow DOM but if you get the HTML for index.html
querySelector('body').innerHTML
the shadow DOM of the elements is not included.
You explicitly need to switch to the shadow DOM of a custom element to get access to that HTML.
Shadow DOM is not about hiding your elements implementation from other developers, it's about hiding it from CSS, JS or other means that might accidentally read or manipulate it.
This allows to break down complexity of the DOM of a whole application to smaller parts that are better manageable.