Thanks guys. Appreciate the suggestions. I will keep these options available for possible future use.
What I have figured out (I think) is that any of these programs read in the data and manipulate it in some sort of internal format and then write it out. So, they have to go through an output formatting stage. As an analogy, from an audio perspective, it would be like opening a flac file, lopping off 10 seconds at the start and then writing it out again. The output would go back through the flac compression. If something like that is what is going on when the video is written out, I might was well let MC do it. As I said, I am not video savvy, but that is my "analysis". I will probably just stick to MC for now.
I did come across an interesting little tool for reading video files form the net, like Facebook. clipconverter.cc takes a url, opens the file and the lets you write it out in all sorts of formats. It also lets you set a start and a stop point. It also has a add-on for browsers. So, using Firefox, whenever viewing something on YouTube, for example, there is an option on the screen to grab the video and write it out in various formats, including adding a start and stop point. Pretty handy. If you want the file in MC, you might as well just use MC to grab a YouTube video and set the start and stop points. But, for files that do not need to be included in MC, clipconverter seems like a nice option.
Thanks again.