RE: DLC/bonus content. If you've not played Peace Walker it might seem a bit odd, but think of Ground Zeroes the location as kinda like a template. You'll have the main Ground Zeroes story mission, scripted and set the way KojiPro intended. And then you'll have the side missions, which are activated separately and use the Ground Zeroes template with alteration for the new objective. Stuff like a different time of day, weather effects, enemy types, location, and patrols, available equipment, etc.
The DLC/bonus stuff is that. You have a new skin to play as, Classic Snake or Raiden, and the Ground Zeroes location is rejigged with new mission design and parameters.