Well I finally got a better idea how the routes work in this game, unfortunately while reading before I overlooked a vital "ない". You simply need to stick with the proper color island every chapter for Nelie/Shiah, Helion, and Nim routes (if their color isn't available that chapter then it doesn't matter which you choose), for some reason the
guide makes it sound more complicated than it is. Thanks to overlooking that negative though, I mistakenly thought I had to stop choosing blue after the first two chapters, spent hours and hours on the painful Chapter 3 red island (totally linear path with lots of unavoidable enemies) only to find myself kicked off Nelie/Shiah route (and missing out on the Normal route scene for that chapter as well), leaving me with no choice but to load my game back to the start of the chapter and waste hours of progress. Blargh.
And I figured out that "Normal route" is where you get the scenes for the characters who don't have their own route; Chapter 3 is Halion/Himika, Chapter 4 is Faren, Chapter 5 is Selia, and Chapter 6 is Nanaru. Once you're on Normal route (i.e. not entering any main routes by the end of Chapter 2) you have to choose the correct island and get the event there in order to get the scene at the end of the chapter.
It's clear that Mula and Zena routes are 2nd+ playthrough only, though I'm not quite sure yet how you enter them. I think Mula route requires an event on a new island that unlocks in Chapter 2 only on 2nd+ playthroughs, then after that it doesn't matter where you go, but the boss fight every chapter gets changed to a special one for her route. Zena route has something to do with using her in battle but I'll have to wait till next playthrough to see exactly how it works.