Ghandar, I concor, from my own experience for video playback, not touching the screen size adjustment is the best practice for correct behaviour. However, I do notice that with viewing the moviesheets (about images in jukebox) now appears zoomed (i.e. top and bottom sections are cropped or a sort of overscan is applied) when not adjusting the screen size for my LCD full HD TV. My about images are all 1280x720. The remainder of the GUI seems to be o.k.
As it was mentioned that the screen size adjustment may be necessary for people with CRT TV's then it may be worthwhile to replace the screen size setting to a TV type selector listing LCD panel, projector and CRT (whereby screen size setting is switch to off when LCD (LED) is selected and upon CRT selection, the user only then will be able to change the screen size as needed.
Although you mention that it was discussed many times on the Mede8er forum, I ,as a very enthousiatic mede8er user, did not stumble on this remedial action until yesterday. My opinion is that it is not common knowledge as the user manual clearly explains the operation differently. The behaviour of the x3D in the screen size issue is also different to that of the previous generation players and therefore adds to the confusion.