Kingdom Come/WMG

The Rorschach seen in the bar is a fanboy.
A Watchmen fanboy, if you hadn't figured that out. Most likely a normal human being, but perhaps a metahuman as well. He read Watchmen and like so many others, identified with Rorschach. Maybe not completely, perhaps just the killing criminals part, or perhaps in every way imaginable. It really doesn't matter. So he created his own Rorschach outfit, most likely with some kevlar or mesh in it for safety. The reason we never see him outside of the Bar scene isn't just because he's a cameo, but because he doesn't get involved in the fight. He stays in whatever city he's from, working the streets and dealing with common crime, staying under everyone's radar. Perhaps he and The Question actually work together (they were seen talking in the bar). Perhaps they're just friends. But no matter what, he avoided the entire conflict and is cleaning up the streets of some city, one criminal at a time.

Alternatively, most of the new heroes are fanboys.
You want to become a hero, but you can't think of a costume or perhaps all your ideas are taken. Many people have favorite characters, and many people want to become their favorite characters. They see a chance, and they take it. Hence why Dr. Strange, Spider-Man and Iron Man are also seen as well as many other fictional characters not from the main DCU. They're fans. Chances are, there's a Faith Lehane, a SPARTAN-117, a Silk Specter and anyone you can think of from before 2006.

In Kingdom Come universe, everything ever having to do with DC period is Canon.
Golden Age one shots from anthology comics? Canon. Obscure characters from The Interregnum? Canon. The Super Friends Cartoon? Canon. Bronze Age counterculture characters? Canon. Watchmen? Canon. The Dark Knight returns? Canon. The Batman movies? Canon. The Batman Animated Series? Canon. Stuff done by Vertigo? Canon. How do we know this? Because we see it in the damn book that's why!
 * You forgot Fat Albert and The Cosby Kids (arrested by Batbots) and several Marvel characters (seen in the background of the final fight scene) are also somehow canon. Although Dark Knight Returns can't be canon, their are ruins of Wayne Manor look smashed no burned and Green Arrow has two arms
 * The Manor could have been rebuilt, and the arm could be bionic or regrown via one of the many mad scientists of The DCU.
 * Actually, in the original script, the Bat knights where supposed to be an army of followers much like the "Sons of Batman" seen in DKR. The Robotic versions weren't to be introduced until later. In fact, many of the things you talked about where last minute changes too. They even cut out a sizable chunk of the first chapter, dealing with the Justice Battalion before the battle in Kansas (which would have been the climax of the first issue), which would have shown Captain Atom as a Dr. Manhattan like figure. When the editorial ordered it shortened down from six issues to four they re-wrote it.
 * Rorschach and The Question are seen talking in the bar. So, perhaps Doc wasn't kidding with the "doubt he'll make it back to civilization". He tossed him into this universe.

Magog is the Antichrist
Make sense in context, the events of the book are Armageddon, Superman is the Christ figure, so Magog is the Antichrist. Either him or Luthor.
 * Of course, why do you think he was named that? It was meant to be symbolic.

Luthor is the Antichrist
See above
 * Doubtful. He wants to rid the world of the super-powered people. Its unlikely he intended for Superman to go berserk.

Superman is the Antichrist
He fell from "heaven", gains power from the sun like a pagan sun-god and shoots fire out of his eyes, his coming marks the end of the world and usually leads to events where cities are destroyed, meteors strike the earth, masses of people disappear, etc. In Kingdom Come he goes out and gathers all the superheroes of the world into one location for Armageddon, makes speeches during a world crisis and tells us that everything will be fine, and he goes berserk at the end in trying to kill the U.N. Brainwashed Billy Batson would probably call him the "king monster."

Kingdome Come takes place in the original universe/timeline, or near original (Flashpoint spoilers)
As seen above, apparently Watchmen, Vertigo, and the DC main universe are canon in Kingdom Come. 1.5 decades later this seems familiar to the ending note of Flashpoint. The universe was fractured into three, and was then put back together. So we once are now seeing a Doctor Manhattan like Captain Atom in the New 52. Vertigo and Wildstorm are now integrated into the DC proper. I.e. DC has become what Kingdom Come was thought to be, with one exception. Kingdom Come was written prior to Wildstorm and their titles being purchased by DC. There are two scenarios.

First, Kingdom Come depicts the pre-split back together universe (which is different due to splitting, allowing changes to occur and remerging). We just don't see the non-yet aquired Wildstorm cast.

Two, Wildstorm was split off first. Watchman is some fragment or shard that gets lost in the splitting process. We see "Under the Hood", Rorschach in Kingdom Come as it is already breaking loose, flapping at the edges. When it breaks away it snaps the fully powered Captain Atom into two. Part of him remains.... him, for lack of a better descriptive. The other part is Doctor Manhattan.