File extension doesn't matter, because both MOV and MP4 don't have any real effect on encoded video quality. They just act like containers.
P.S. The choice between MOV and MP4 is quite simple, based on the place where you need to play the resulting videos. Ideally, if you're using Mac, MOV is quite safe and efficient；However, to play on non-Apple devices, MP4 proves to be a much better option. Of course, you can choose to convert MOV to MP4 or vice verse with this easy-to-use DRmare Video Converter.