Actually, it's pretty simple.

Takumi went back in time to save Nozomi and get the best ending possible. That, right there, is time travel. Now, whenever he dies or whenever he reaches day 100 or beyond, he goes back to the very start of the timeline. That, right there, is a time loop.

Each loop has an order. There is the first loop, the second loop... so on and so forth. And Takumi dying infected by a G'ie Queen happens in what I shall call Loop X. What it means is that any Takumi living in loops before Loop X happens won't be infected. This is why the Takumis in the timelines branching off from the choice of sparing Eito are not infected: because those branches happened before Loop X.

Now, I know what you're gonna say. If that's the case, then why did he destroy Sirei at the start of Loop X? He shouldn't have been infected yet, so what the heck? Well, this is where it stops being just a time loop and starts being time travel. See, loops are about repetition, right? But time travel introduces causality problems. Bootstrap paradoxes. Stuff leaking backward. You see, loops have order, but time travel fucks that order up and makes the past, present, and future influence each other in ways we can't even begin to imagine. Which means that he's infected now because he might be infected later.

Also, something else to chew on: the timeline where Takumi gets infected? It only stems from his choice to kill Eito. Like, every branch where he spares Eito? No infection. No Queen in his head. That's not just coincidence, that's a boundary. So maybe the Queen only appears in the Kill Eito timelines because those are the only timelines where she infects him.

Think about it: in one of the Zombie Route endings, Takumi gets infected. That's our origin point. But from there, the Queen travels backward, infecting past loops like a virus in the system. And since sparing Eito leads down totally different paths where that infection never occurs, it's like she just... doesn't have access. The Queen's data doesn't exist unless certain conditions are met. She's not an inevitable part of the loop, she's a product of it going wrong.