You've read that exchange more carefully than most, and you're right to single it out. Mister D's offer is engineered to land on Mezenga's deepest fear, and the fear is specifically the eternal separation from the only source of emotional comfort he's known, Enzo. That's exactly what the scene is doing. So your instinct isn't wrong.
But I'd push back on the conclusion that it means he didn't care about the others.
The souls aren't kept by Mezenga the way a collector keeps things. They're held intact. Pulsing. Preserved.
And I suppose that's the cruelty of the bargain. And it's deliberate. Mister D doesn't offer Mezenga a clean villain's choice. He offers him a choice where mercy and predation wear the same face. Mezenga continuing is, simultaneously, the most selfish thing he can do (he keeps Enzo in some form) and the most merciful (he keeps everyone else in the process). The story never lets you separate those two. Because two things can be true at once.
That's the whole tragedy of Theron.
He's a victim of his own choices.
Now... I'd just gently suggest you keep an eye on something: the tree is not a separate thing from Theron. It's an extension of him. One can't live without the other. And if that's true, then the question of what kind of "life force" the tree reaches for, Enzo's, or in the case of this chapter, Luka and Devin's "love force", may not be as arbitrary as it looks...