It does. There's an interview with Jim Sorenson on RFC #400 and the answer to the question, what's the difference between this and the original two volumes? is that: it isn't the two books back to back, they've been integrated and reorganised; errors and typos from the original books have been fixed; the 22 additional pages produced for Botcon & the club magazine are included; there are an additional six new pages on top of that, taking the page count to something like 472 pages overall.
Although he was a bit shady on what the six new pages are. At one point it sounded like new extra stuff from season four, at another it sounded like he was saying they're heavily revised/improved/expanded pages from the first prints.
I got my copy yesterday, and it is quite wonderful. ALL the club stuff has been added, all the supplemental stuff Wyatt has done has been added, it goes into more details about things not mentioned or barely touched in the first and second volumes. New concept art I don't recall being in the first volume. New content has been generated, combined with Sorenson's artwork in wyatt's style has dramatically improved. (Recall the abysmal Cheetor and Skybyte headshots that cameoed in volume two, verses the new wyatt designs that were generated since).
On the downside, stuff was removed. Almost all references to franchises outside of TF have been removed. No Doctor Who references at all. The Star Trek references have been mildly altered. The gobot (though cykill does cameo), thundercats, and heman references were removed. A Babylon 5 reference remains (possibly because it's so obsure no one policing it caught it), in the form of Z'ha'dum appearing in the star map. As do Melmac and Ork. And apparently Maccadam's serves Mudder's Milk. I haven't read the book back and fourth, but I've not been able to find the sections talking about the multiverse, beyond a section on Animated Shattered Glass. I've also not seen any references to the movieverse, like There were in volume 2.
Added are a ton of references to IDW, as Rung and Swerve cameo, and there are several references to someone called pharma. Actually, almost all new content that's generated specifically for the book are IDW call outs. Prime Knockout, and NuRid Strongarm make cameos.