Is the beginning scene the only seen that truly happens

Yes, it happens (or something very like it, anyway). However, how much of the rest of the film actually happened is open to debate. Verbal needs to concoct a story that will tie in with what Kujan and the police already know, so he can't change essential facts all that much in terms of what happened aboard the ship, for example. Having said that, he must have known that Kujan would cotton on to the false names before very long, so he wasn't all that concerned with it standing up in every detail to subsequent scrutiny - e.g. did the shooting in the car park, or the raid on the 'New York Taxi Service' ever happen? What Verbal was doing was to create as much confusion and doubt about what actually events as possible, so he came up with a story that he knew would not last for more than a few hours, but by then, he would be long gone and nobody would really know what had happened. (Remember that he had no way of knowing about the survivor's statement.)

The opening scene is the only one not told from the perspective of Verbal (or Kujan), so it's the only one we know that really took place.

It's the only scene that we know happened for 100% certain. But at least some of the other things he told have to be true, too. The line-up, the taxi service, knowing that a figure named Keyser Soze was after them, Keaton's girlfriend/wife being held at her will, etc. He may have lied about a lot of the details and in some cases just outright fabricated things, but there had to be a lot of truth in what he said, too.

To me a big part of the whole conceit of the story is that we can never know what really did happen, within the fictional story contained here, and what was entirely fabricated by Verbal. We can make some pretty good guesses but never be sure, because it doesn't really matter. What matters is Verbal and who he really is and how he deals with Kujon "who is smarter than Verbal" as he is fond of saying.

..*.. TxMike ..*..
Sometimes I think we're alone in the universe, and sometimes not.

I've always presumed that it is. I think it conceivably could (perhaps at a stretch) be considered part of Verbal's testimony to the D.A. - the sequence concludes with the push-in shot on the barrels, which then dissolves onto a shot of Verbal making his statement. That kind of film-language often means to associate things. What is inconceivable is that Verbal would have alluded to what Soze and Keaton said to one another before Soze shoots Keaton and sets the deck on fire. But then, on the other hand, there are a few other scenes, which decidedly are narrated by Verbal, that show conversations that he couldn't have been in a position to recount.

No, lots of Verbal's story actually happens, while lots is made up in Kujan's office. The first scene actually happens. Scenes with Redfoot and Kobayashi, for instance except for the final one (and in which the man's name is unknown), do not happen.