Nope. It was Versus Books, a small company that did more "independent" game guides. I really wish versus had kept up their work. I bought the guide more because it was fun and enjoyable to read then because I actually needed it.
Yeah, no problem. The question mark was used to list Pokemon they didn't want to spoil for you. Then later there was a section in the back of the book where the writers tied up loose ends. One of the loose ends was that even if you caught every Pokemon the book talks about there will be some missing. The picture associated with this section was Gold coming across a question mark. The missing pokemon are: the kanto starters, the fossils, and the legendaries (the list is right next to the "question mark" picture in the section). Someone's memory has distorted and they are now associating the question mark picture for legendaries and the missing Pokemon from the game with the question marks (Larvitar and Misdreavus) on the Mt. Silver pokemon roster.
I think Blue is the only real challenge among the Kanto Gym leaders. If you don't OHKO Exeggutor and it uses Trick Room, you'll be at a severe disadvantage because it's likely his Pokemon will be slower.
I mean, I love how Johto and Kanto (okay, mostly Johto) look in Gen 4. And there's lots of daily/weekly tasks to do in the post-game. But it's so damn painful and annoying just to complete the damn game, and the lack of a VS Seeker doesn't help at all.
Don't ever bring this up publicly on the forums though, or you'll be marauded by nostalgia freaks.