If you convert an iDVD-made DVD into a video file like an MP4, just like when you convert any other DVD, you'll lose all the menus, navigation, and other "special features." The video files don't generally support any of that. So your converted MP4 will be basically just the main title, like if you Handbraked a movie.
On the other hand, if you want everything -- the navigation and menus and so on, just save the DVD contents (the VIDEO_TS, AUDIO_TS, etc folders) in a folder anywhere on your HD. If you point VLC (any platform) or DVD Player at them, then they will play the VIDEO_TS folder just as if it were a DVD.