I finished the audio commentary with Brett Ratner, Simon Kinberg and Zak Penn. There's only one more mention of Cyclops in the film, and it comes at the end when we pan across the gravestones...
Zak: "You know, some people, some of the fans online feel like we should've given Scott more of a tribute... "
Simon: "Well, they're Scott fans."
Zak: "Right. They're Scott fans."
And that's it. They immediate segue from that into how pissed they are about Beast going to the UN instead of staying at the school, while Ratner tries to defend it.
There is one other hilarious moment in the commentary, though, where they mention how one thing they disagreed with the fans on was how much they loved Halle Berry's portrayal of Storm, so they said they increased her role because of how much they liked her. It's amusing that they acknowledge for the whole world to hear that most people didn't like Halle in these movies. Plus, um, I thought her role was increased because she demanded it? Maybe they're just trying to be diplomatic, whatever.