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She will not trigger any intermission(grey) levels. However, I've only tested this for the following one and not the Gravitron.
After I rescued her, the game said "LEVEL COMPLETE: All crew members rescued!". Violet then gave her speech about the lost crew members and teleporters.
After the speech, all members except Viridian and Violet were missing again. I teleported to the end of the Red Tower, but Vermilion was not there. I then decided to go through the tower again. Vermilion was still not there. The crew members were not on the ship either. Apparently, after rescuing them once, they won't appear again.
And because of that, I have just wasted around 20 minutes of my life making the game unwinnable. If I find any new observations, I'll post them in this thread.
I don't even know anymore. 3DS FC: 2320-6426-2982 | Pokemon X IGN: Tab