Having used Split Infinity's guide since the 3rd or 4th, based upon what I've gone through, the major thing that I've discovered is that the guide skips over the Kolton experience, before the final boss.
Since you don't go back to Kolton you also don't view the 'Secret of _' events, which means you can't unlock IC level 6. It appears you can still unlock these in the end-game, however.
There's minor mistakes in what awards you receive for doing certain things, but these really are relatively minor (in my opinion). (There is one that has a bigger reward than advertised, but it's tied to an achievement, so it's unlikely to cause too much trouble.)
The sidequest-specific FAQ on GameFAQs seems to have been ripped directly from the official guide, and Split Infinity numbers his differently. Michelle's Lover (SI's #15) appears to be missing from the official guide, but the reward isn't unique, and completing all sidequests isn't an achievement.
I've found the Hints and Tips guide on GameFAQs to be useful for missable items (despite that I'm not even going to try getting all items).
At this point, I believe I can say the only key point is to travel back to Kolton before heading on to the Underwater Palace. Of course, if you're just in it for the story, you should be fine with the official book. And if you want to get every item for the achievement, you'll obviously want to use a fan-crafted FAQ.