I’d assume the problem is not being able to separate the dialog/sfx from the music, which in the case of making a radically altered cut of a film is especially troublesome; because the changes in the score (even when helped by fades) make the editing evident, and gets in the way of enjoying a fan edit (happens far too often). To be fair, I don’t mind muting some portions of the film, it’s a perfectly acceptable technique associated with the restoration of lost scenes, the same as using stills or reverting to B&W footage; even using explainatory cards when nothing else is available. The downside is that the cut is admiting to be incomplete, but it’s better than nothing.

In my mind, for instance, such methods could apply to radical prequel edits; to present them as restorations of partially lost movies or with missing elements. Certainly doesn’t hurt to experiment in that regard.