The discussions in this thread regarding the place of Alternative's epilogue have convinced me to try to crystallize the ideas floating around in my head regarding it. I owe much of what follows to the discussions I've had with other members of the fandom who remain nameless to this day, across three certain places on the Internet, and by reading old discussions of the trilogy. The discussions held at HongFire when Muv-Luv Alternative originally came out in February 2006 are of particular importance, although it is very unfortunate that the complete set of discussions did not appear to survive the vagaries of time.Unless someone here participated in those discussions all those years ago Spoilers for the trilogy, and I will be referencing in passing some plot elements from both Puella Magi Madoka Magica and Metal Gear Solid V: The Phantom Pain, so there are some spoilers for them too.
Tl;dr: I'll attempt to show that from the point of view of seeing Alternative as a science fiction, coming-of-age war story for Takeru with Extra and Unlimited as its (maybe yes, maybe not so much) needed prequels, what happens at the very end of Chapter 10 of Alternative is a fitting, though bittersweet, end to the trilogy and the epilogue appears something which is tacked on, while on the other, looking at how the trilogy as a single, massive work, and how it is structured, that it is unfair for the epilogue to be labeled as such, and that it in fact strongly ties up with the trilogy as a whole. For one reason or the other, my thoughts regarding the latter came out more easily, and thus I'll be covering it first; I'll put down the other perspective later once I organize it.
The next part is to follow later, although I want to offer the first part to you to (maybe) stimulate some discussion.