One of the few complaints some people have with Revelation was the Ret-Con of the Trap books into Prison Ages. However, this Ret-Con is in fact where the game gets it's title from. It's the Revelation that Sirius and Achanar still live. Furthermore, at the start of Riven, Atrus gives the player a notebook with some important information, including how trap books are made and work. By altering a small line of text in a regular linking book, the link can be broken. Anyone who tries to use that book is caught in limbo between ages. If the change is reversed, the link is repaired, and the person trapped is then sent to where the book links to.
Spire and Haven are each a fusion of two of the four main ages of the original Myst. Spire has the crystals and desolation of Selenitic and the technology of Mechanical. Haven has a shipwreck like Stoneship and is a low-tech nature-filled age like Channelwood.
The game's three ages for a trinity. Appropriately for their logically-minded author, Spire and Haven represent the two basic branches of natural science: physical science and life science. Serenia, an age of Catherine's, rounds out the trio by representing spirituality.
The first Fridge Brilliance entry leads to more Fridge horror as you understand the sequence of events.
Sirius and Achenar are trapped in an interdimensional limbo for a while in the library books.
In the end of the first game, Atrus fixes the books, freeing them to go to their worlds, then burns the linking books.
The brothers get a Hope Spot as they are sent to their respective ages, thinking they can link back if they can only find the book. THEN they break down and go mad.
Further fridge horror comes when you realize that linking books are large, handwritten books (at a minimum 50 pages) containing detailed descriptions of worlds, and a single error can make it an inescapable trap. Now, programmers: when was the last time you wrote unbugged code on the first try?