Hello, anon! Both guides are quite similar, with the main difference being the overall layout.
3DS Edition Official Complete Guide is 608 pages and has six chapters chapters: System, Battle, Story, Subevents, Data, and Extra.
System covers basic game features and mechanics such as cooking and the Town Link system. Battle covers things like AD Skills, capacity cores, and the party’s artes. Story is essentially a walkthrough with maps, brief enemy and sidequest notes. Subevents is a supplement to the walkthrough and covers sidequests in details. Data details items, shops, recipes, titles, skits, and a bestiary.
Extra illustrates various world-building information such as fomicry and the planet storm with concept art, comments on different character relationships, and a list of characters in a short directory (this is where Ginji and Noelle’s last name comes from.) An illustration gallery with character art, cut-ins, and a few skit faces for everyone. There’s also costume rough drafts, art and concept roughs for important side characters such as Peony, Nebilim, Mary, etc. The final part is a special interview with the seiyuu of Luke/Asch and Tear.
3DS Perfect Guide is 511 pages and has the same general information, but with battle details combined into the system category.
Almost a hundred pages shorter, it’s more condensed with a different layout and maps, and smaller text. Though it quotes Luke’s diary throughput the walkthrough and features a small screenshot of everyone from the character disk in Yulia City. While the extras cover some of the same information, such as the planet storm, but with different diagrams and plenty of new concept art. (Sadly, most of these are incredibly tiny, hence the low quality of my scans.) This book has a timeline, more skit faces and character-defining moments for each party member, God-General, plus Ion and Van. The last difference is a ‘biographical and words dictionary’ with little blurbs on everything from the blue gorgonhod swallowtail to Sylvia, some even with small illustrations.
Both books have a rating of four and half stars on Amazon Japan, though one review notes the Perfect Guide has a number of typographical errors. Overall, you can’t go wrong with either one if you want a reference to help you through the game or to indulge in the various extras!