It depends, I guess.
I understand that the matter of debate was if using a new character with no connection to the past villain is a good move. In Exile could legitimately argue that a person who first experienced the Mass Effect universe through the book could say it was unsatisfying to use Shepard instead of Anderson in the games.
Since Shepard is a beloved protagonist for many players who won't agree with that opinion, some could argue that in the end it's a matter of what works in the final game, not a point of "narrative principle". That unless we argue:
1. That being forced to play as Shepard was indeed a disservice to those who read the book first.
2. That such an opinion doesn't count because only a handful would be in that situation (an appeal to popularity).
3. That such an opinion doesn't count because book experience is inferior to game experience.
If I'm not mistaken (correct me if I am), I think the later is your case. "Reading about Anderson in a novel is not like playing as Anderson in a game". As you yourself say, whether that it's a rule or just one option is a matter of debate. Which means that, for those who agree with your stance, that Anderson's book came before or after makes no difference to the argument. However, for those who don't agree, the book does indeed make a difference.
TL;DR: Do you consider all stories equal? Then the book counts. You don't? Then the book doesn't count.
I'm the last person who would ever suggest that book experience is 'inferior' to game experience. I love books. I read at least 3 every month, and good ones too.
But all stories are NOT equal. A novel is not a movie. A tv series is not a comic book. Every medium demands different narrative techniques. A movie is not experienced in the same way as a novel, which is why the adaptation of a story from a book to a movie is not a copy, but a unique work in its own right, based on the original material. People who say that they haven't read X book, 'but they've seen the movie' are simply being ignorant. It's like saying that you've never been to Paris, but you've seen it on TV and you think it's the same thing.
When did I say that one was 'inferior'? There are very good movies based on very bad books, and vice-versa, and so too for plays, tv series, comic-books, games, etc. Each is a different art form, experienced differently. They have different relationships of time and space, different approaches to structure and theme, and different connections to the reader / audience.
That's why some works are said to be 'unfilmable', like the stories of Jorge Luis Borges, for example. On the other hand, 'Rosencranz and Guildenstern Are Dead' would be a pretty bad novel. It's a play about the nature of reality within a play, it wouldn't work outside of that context. It was adapted into a fantastic movie, and yet the movie is not the play. The movie 'Watchmen' is practically a frame-for-frame reproduction of the comic-book 'Watchmen', and yet it manages to completely miss the point of it. Why? Because Scott Snyder doesn't understand this. Charlie Kaufman does understand it, and that's what 'Adaptation' and 'Being John Malkovich' are all about.
What I'm saying is that 'watching John Malkovich' isn't the same as 'being John Malkovich' or 'reading about John Malkovich'. Or in this case, 'being David Anderson'.
TL;DR: Why would I bother to explain complex things if I assumed you were too lazy or dull to read them, and provide you with a condescending TL;DR? That would be an insult to your intelligence.