Okay, thanks.

Or maybe they’re the ones who are whole because they have the self-awareness to define themselves after everything and everyone was turned to primordial goop.

Human Instrumentality begins, sucking everyone up into oneness, but right afterwards Shinji says “no, this isn’t right”, and Lilith instead sets people’s souls to be, I guess, free-floating. The choice that you mentioned is during this part, and it’s whether everyone’s souls can return to human bodies. So it’s kind of like two different half-states because Shinji was indecisive. The way I interpreted the ending was that Shinji and Asuka were the first humans to return to their bodies because they sorted out their feelings and chose life (Asuka having done so in the first half of the movie, when she pilots Unit-02 again).

I'm no authority of Eva either, but the intended takeaway of the series is the exact opposite of what you're saying.

A core lesson in evangelion is that pain, misunderstandings, confusion, insecurity, and anger are all important aspects of being human. Confronting these feelings and making peace with the fact that sorrow is as valid a human emotion as joy is what will make you content in this world.

Instrumentality was alluring specifically because it "fixed" the sources of dissatisfaction. It fixed insecurity. It fixed anger. It fixed loneliness. But in actuality, the zero sum nature of instrumentality means that, in order to remove negative emotions, you also remove the positive ones too. It means sacrificing all individual feelings for absolute contentedness.

This is what Shinji had to confront when instrumentality began. And instead of running from his problems like he and others did throughout the show, both literally and figuratively, he confronted them. He accepted what he had to do to live a fulfilling, albeit tumultuous, life. Which is why he and Asuka appear on the shore. Of all humanity, they were the first to make peace with the nature of their existence and resurface as individuals.

and by leaving, they leave the oneness of their “new garden of eden”, tasting the fruit and embracing separateness and beginning the universe anew

It's true that this is a common theme in Evangelion, but Hideki Anno explicitly rejects this sort of thinking. The whole message of Evangelion is to accept yourself as an individual, with flaws, and to work to change and better yourself with other people, and to form real relationships with them. As is clear from the show, Instrumentality isn't a natural thing. It's not a religious reward. It's fool's gold. Rather than real happiness pursued with other real people, you simply lose all individuality. What's another way of saying you become one with the universe? You die and return to dust. That's all the people who remained in Instrumentality did. To be happy, you must first be, and you qua you cannot be unless you exist as an individual. Otherwise, there's an amorphous blob of happiness, maybe, but it's no better than suicide as you, the self, are gone.