MAUI - How to merge flyout navigation with navigation from code - GoToAsync()?

I have a problem with navigating from code and from flyout at the same time. It seems like they are 2 different systems. I could describe my problem as this: Flyout is navigating between pages but GoToAsync() is changing the content of the page to a different one but not the page itself. It looks like a flyout navigates to a group of pages and GoToAsync() navigates between single pages in the active group.