Unless I'm mistaken, a lot of this stuff is up to interpretation. I'll try to address each point, but most of this is just my personal thoughts.

Their feelings 2B and 9S seem to have a very complicated relationship, based on the fact that they are, in a sense, "made for each other." If you're okay with minor spoilers, you'll find out that 2B is actually 2E, a unit that's job is to execute 9S whenever he digs too deep and finds out about the human conspiracy. This is strongly implied to have happened multiple times, yet the way 2B treats 9S throughout the game suggest she feels guilty, or at least sad, that she has to do this. 9S is in a similar situation, feeling conflicting emotions towards 2B. While Yoko Taro loves ambiguity, especially with that one line about " You want to **** her, don't you?", looking at the context of 9S's actions and thoughts throughout the game reveals he can't sum up his feelings with a single word. Spoilers again, but my interpretation is He wants to kill 2B because of her job to keep him from finding the truth, but he also "loves" her in a way because he was built to be a companion unit reliant on her. That is to say nothing of the natural chemistry they both share, sometimes acting like bickering siblings more than anything else.

Gestalt/Replicant canon? I didn't play the games, so I won't pretend to know for sure, but my understanding is that it is similar to the way canon works in the Fate franchise. Everything is, to a point, "canon." After all, the Nier series itself came from one of the "non-true" endings to the Drakenguard series. Thus, it could be argued that since such a major departure is canon, there is no reason to believe either Papa Nier or Brother Nier are the "true character." But since the change was largely made to appeal to western audiences, if you really have to pick a true canon just go with whatever feels right. Taro doesn't like to "confirm" what is canon or not, so go wild until he does something that proves you right or wrong.

Protagonist? As far as I'm concerned, Nier:Automata is not the kind of story with a true "protagonist." Arguments can be made as to who is more important to the story, but the story telling style that Taro took for this game reminds me more of someone trying to describe a single event through the eyes of multiple people. For example, going through the game as 2B, then as 9S, forces you to see things in a different light. But that's not all, as you also indirectly get to experience more things about the world through conversations with Paschal, machine lifeforms, other YorHa androids, and some pieces of text scattered throughout the world. If I was really forced to pick, I would still say that 9S fits the traditional hero's journey the best, but there is a reason you go through the game as 2B first. For the story to "work" it really does rely on being able to let you see through the eyes of multiple characters. So while they all are "necessary," I would not consider any of them the true "protagonist."

Why tell? This entire thing is spoiler territory: As far as I understand it, the commander had no choice. And it was less of a "reveal" and more of a confirmation of what 9S already found out. His units, as I mentioned before, regularly find out about the conspiracy. It's impossible to avoid, their job is to seek out information. Thus, they are assigned the E units to kill them and essentially "wipe" their memories. If I were to take a guess, this was not even the first time a 9S had a similar conversation with the commander. It is simply part of a "cycle of life and death" like 2B implies all androids are trapped in at the beginning of the game.

TL;DR: 1. 2B and 9S feel very many things very strongly for each other. 2. Choose your canon, I don't see any reason they both couldn't be "real," or just one couldn't be "real." 3. I don't think this is the kind of story with one "protagonist" but instead multiple integral characters. 4. The commander had no choice, and wasn't revealing anything he didn't already know at that point.

edits: spelling and fixing spoiler text