Save as self-contained movie

Every time I edit a movie, whether it be .avi, .wmv, .divx, .mov, .mp4, .mpg, .ram, or .swf, when I go to save the changes, QuickTime makes me save it as a "self-contained movie" which is .mov. Is there a way to save an edited movie file as it's original file type. Like if I edited a .mp4 movie can I save it as a .mp4 movie after making changes? This is a pain because every time I want to edit a movie on my iPhone (which .mp4 the only compatible type, I think...) I have to save it as a .mov movie, and then export it to .mp4 (which take FOREVER if you are editing a 2 hour long movie). Thanks!