The master track is used to control the whole project. All of the tracks in your project are eventually routed through the master track. This can allow you to put effects on the entire song or to utilize some volume automation, which can be particularly useful for a song that has a fade out at the end. When recording in a professional setting, you typically have the engineer mix the song, then it gets passed to a mastering engineer, who is essentially adding any of these effects/automation. It's generally not advised to be adding effects to your master track if you don't know what you're doing, as it can drastically change your whole mix. The only real reason I ever add effects is to place a limiter on the whole song and boost the gain so that I can export a higher volume track for listening. I'm not releasing anything professionally and if I were, I would not be taking that approach but hiring someone who really knows what they're doing to handle the mastering.
The master track appearing there would not affect anything to do with being able to bounce the project down. It is always there, just hidden. Your bouncing issues likely have to do with some settings or what area of the song you are bouncing. I typically will use the cycle region function to cover the whole song, then bounce.