I believe that they ARE real choices. They let you say something about your character and the way they interact with the world. I don't feel that just because the outcome is the same in the grand scale, that makes the choice any less real, especially if in the game itself things are impacted.
Honestly I've come to believe that those sorts of things are genuinely fine and the kind of series-long reverberations we dream of just aren't posible yet. Garrus has to be on Omega for the game. They don't have the time or money to make entirely new quests for him based on your interactions in the first game, because that would reverberate through not just the rest of 2, but potentially into 3 as well. Then you have to take into account doing that for every other companion. How can they practically avoid that without either blowing open the scope of the game to ridiculous levels, or just not including Garrus at all? Or worse, never include the choice in the first place so they don't have to wrangle the possible outcomes? I find personally that the real value of choice in a game is that I'm able to express my character and roleplay in the game, regardless of how static or not the reaction is. I'd rather be able to greet someone in three different ways and get the same reaction than only greet them one way. It's why I love Wrath of the Righteous so much. In one playthrough I was able t most recent playthrough, I was so enthralled with my character I wrote out her eventual religion and place in the history of the world. That's never gonna come up in a sequel and I'm fine with that. It's better than the game deciding that I didn't make the choice I did.