The file structure on DVDs has nothing to do with chapters. When you author a DVD, you have a large MPEG for each title, and the authoring program lets you specify times for chapters. It splits the MPEG up just so as not to go over the 1GB single file limit of the UDF file system.
Many TV DVDs, however, have each episode as a separate title, and titles often are stored in separate files (or groups of files if they go over 1 GB each).
Many DVD decryptors only show you the disk based on the DVD structure instead of the file structure, because it makes more sense and because that's the way libdvdread functions. Among these are 0SEx and YADE.