Yes because your page is located under mywebsite folder…
In your tracking, you just have to set the url as https://domain.com/my-page.html instead of https://domain.com/mywebsite/my-page.html
Isn’t a bit “hacky” ? Is there no other way to tell Matomo that the root website in in a folder (domain.com/mywebsite) and not a root domain (domain.com) ?