Normally, in the developing proccess of a AAA videogame, hundreds of lines of code, concept art, ideas, levels, models, missions, etc are scrapped before the final and comercial build. Either for a lack of time, budget, or conflicting ideas inside the Dev Team, those ideas are left behind, and rarely spoken about again.

KojiPro never lacked time.

KojiPro never lacked a budget.

We know about cut content. Chaper 3 PEACE, Camp Omega, some cutscenes. However, none of those issues has never been adressed by KojiPro or Konami directly. We still don't know what happened to Camp Omega, were is Chapter 3. The point is that being so important issues, no body has said a word about them.

Instead, in a Collector's disc, they wrap a "Phantom" Episode for a game called "The Phantom Pain". How convenient. However, I doubt that Mission 51 is the only lost mission. Why focus on this one? It doesn't try to wrap up the plot, it just leave us with more questions. Scrapped because it wasn't fun? Then half of Chapter 2 should have been scrapped by that logic. Then why not a cutscene, or a cassette tape? Then why Eli's escape story arc is still there, and not scrapped along with the rest of Mission 51?

My answer? The Mission 51 we know is not the real Mission 51. The importance of explaining why Mission 51 was cut is very small compared to things wildly known as Camp Omega. "Mission 51" is either a distractor to something bigger..., or a way to try to apologize for the lack of material in the game, by saying "but we had a lot of cool ideas in our heads!".