Das Boot is more accurate than the propaganda videos you've seen. To answer this part: "yet when i see video of uboats attacking etc the captain uses the periscope in the command room where the navigator is", you have to remember that the Conning tower is very crowded. During an attack, the cameraman would not have any room. Plus the standard procedure was to close the tower hatch and throw an oily rag at the cameraman if he bothered the crew during life and death situations
As to Webster's post, there have been many annoying questions (not like this one) about why some MODS didn't behave like some saw in Das Boot. That was annoying indeed and sparked fury against an otherwise superb movie.