I won't deny that there is a lot of dichotomy expressed throughout the game... Inevitable since the whole thing was designed to present some diametrically opposing choices to the player. The before or after death debate about the meaning of Tennyson's "Ulysses" rages on even to this day... and, honestly, I don't want to get into here. There are references in the game that can be validly taken by players "either way"... and that's the whole point. People keep looking for a definitive, direct from Bioware "win" scenario, but they spent the entire trilogy trying to avoid giving the player just that.
For me, the interpretation that best fits is that whatever happens with the Reaper threat happens AFTER Shepard dies. His death prevents him from completing his mission (regardless of however he would have liked to complete that mission). The endings reflect whatever that desire of his was (based on however the player wanted to (and had) developed his character). What actually happened is unknown... even to Shepard... because he died reaching for that console.
Because I also interpret Tennyson's poem to be reflective (Ulysses deciding whether he had done any "work of noble note" just as he's dying), this fits perfect (again, for me) with my interpretation of MEs endings (all of them). The Catalyst is just a theatrical tool Bioware used to recap what sort leanings (particularly regarding forms of "governing") Shepard might have. I change my ending (Shep's desire about what he wanted to do) depending on how a build my Shepard's character (HIS Soul). I can now happily just leave it up to Bioware to decide if or how my companions resolved the Reaper threat. In all instances, my choices mattered to my Shepard at the moment he died... He WAS the captain of HIS soul.
PS: Shep doesn't have to choose what the Catalyst doles out... he can refuse to choose.
The dichotomy is part of the problem. Many people played Shepard many different ways. And Bioware decided that unless you played your Shepard their way, you did it wrong. To illustrate my point, look at how "default Shepard" plays out, and the outcomes seem much more fitting than that of anyone who actually had a "good"import. And yet, no matter how much of a difference Shepard makes, it's never enough. Hope and optimism dangles before Shep's eyes only to be snatched away by "Art"
There should have been "good" outcomes. There should have been "bad" outcomes. There should have been "bittersweet" outcomes, all based on the narrative woven throughout the game. But Bioware instead chose to weave a single theme into all endings, and blamed the player for not going along with this BS.
Shepard's death, or apparent death, or whatever should never have been a requirement for the ending. Certainly as a possible outcome. Or several outcomes, even. Not everyone wants Shepard to be Ulysses. Just someone who gets the job done and goes home.
Home is behind, the world ahead,
And there are many paths to tread
Through shadows to the edge of night,
Until the stars are all alight.
The world behind and home ahead,
We'll wander back to home and bed.
Mist and twilight, cloud and shade,
Away shall fade! Away shall fade!
Fire and lamp, and meat and bread,
And then to bed! And then to bed!
And as far as I'm concerned, every choice the Catalyst graciously allows Shepard to make is a different way to damn his soul, if you'll excuse the expression. So I'm not to sure what Shepard is captaining, save a sinking ship. Yes, Shepard can "choose" to refuse. But Bioware extends an enormous middle finger to anyone foolish enough to go THAT route.