It's all / and. That's a good call about Decker being the one who is probably a step ahead of The Gang. (I like Decker. Kirk liked Decker too. It was just a bad situation.)Were it not for the following, I'd agree, wholeheartedly in fact, that it's pretty clearly to be with Ilia.
It's Decker who answers the question of what more is there besides the universe. Decker is the one who interprets the probe's statement of intention to join with the creator as physical joining. There's no dialog in between his description of what there is beyond the universe and his declaration of intent to join. He doesn't mention Ilia. So, the biggest problem is that, on paper, it reads like, Higher levels of being? Hell, yeah, let's do this.
Even after, they talk about the birth of a new life form. No one expresses hope that Decker and Ilia have been reunited. The only significant thing happening worth talking about is the machine evolving to a higher plane of existence and a possible next step in the human adventure that's just beginning. Decker and Ilia are just missing, again another blank.
Spock does mention it being the next step in our evolution. Decker and Ilia are guides. Companions, I suppose. (Not in a Doctor Who sense. Definitely not in a Firefly sense.)
But the heart of the scene is Decker looking at Ilia like "Hey, we're going to get ALL OF IT."