I followed the development of the R2 1/350 Enterprise on Hobbytalk as well as received updates on the kit's progress (prior to release) because I was one of the 1701 Club members to get a Premire version of the kit. Gary Kerr, who researched the TOS E for the model (and is now working on the Galileo shuttlecraft kit) mentioned that there had been some talk of adding a light effect to the inboard sides of the nacelles, but it was deemed to expensive to go back and rework the 11 footer so the idea was dropped. It doesn't look like they were hellbent on doing it, but for the sake of completion R2 decided to include the option for lit nacelles for those who might like to explore the "what if" option.
I enjoy thinking that was because of my suggestion to Gary that they make the trench grills separate parts molded in clear, which triggered an insane tirade from another poster who was an "expert" on plastic molding and insisted such a thing would make the kit cost skyrocket and the nacelles become too fragile. That poster's tirades pissed Gary off and made him WANT to do the trenches as separate parts just to piss HIM off.