This is an issue for movie discs too. Some mkv rips will preserve chapter data (though player support is spotty), but in the end it's still a big linear file— menus, intros, trailers, optional features, etc are all gone once it's ripped unless you rip that stuff to separate video files.

Which I get on the one hand, but it's a bummer that in all these cases (CD, DVD, Blu-Ray) the metadata for the larger structure of the production got inextricably tied to the specific physical media implementing it, such that the only real way to preserve that data was to rip a full disc copy.