I believe it is added to the library at the same time so that it will be the same book as any future conversion (preventing confusion if you convert multiple times and the settings changed, "why does each of my devices have a different book on it"
). Additionally, it speeds up future sending.
There is no way to differentiate it, as they are the same MOBI. However, if you select a number of books and send them, you can then remove the MOBI format from them. There is also a Save To Format plugin.