The simplest explanation is that Travis’ inclusion might’ve been a little awkward, narratively speaking. If Travis was included in the hallucination, would he be the adult Travis who died at the start of the series, or teen Travis? From Natalie’s perspective, adult Travis makes the most sense. Natalie’s had an ongoing relationship with Travis post-rescue (something she hasn’t had with Lottie), and it’s been adult Travis’ circumstances she’s been most worried about. The problem is that viewers have never really cared about adult Travis, to the point where it likely would’ve taken us a moment or two to even recognize him.
If the show did decide to include Travis in the plane hallucination, it would’ve most likely been teen Travis. Would that have worked? Maybe, but it would’ve taken the focus away from Javi and Lottie, the characters Natalie’s storyline has revolved around the most in the last two episodes. There’s also the issue that Travis isn’t a consistently comforting figure to Natalie. Javi has always been nice to her and Lottie’s always tried to be supportive, but Travis has gone through several periods of sullen, closed-off behavior. There are three seasons to go and a lot more heartbreak to come, so maybe Travis and Natalie’s relationship takes some even darker turns from here.
Most importantly, however, is that with Javi dead in both timelines, his relationship with Natalie is at an end. Meanwhile, Travis and Natalie are still a vital part of the teen timeline, a storyline the writers still want us to care about going forward. It might make sense for adult Natalie to say goodbye to Travis in her final moments, but for the show itself, this would be a premature farewell. The two’s fates may be sealed, but their stories are still far from over.