Hmmm. You raise some interesting points
Hemiola, and I'm gonna address them from a 'this is what I took from the non-explainy explanation and I'm probably totally wrong' POV, 'cause I ended up with a totally different view of things. Lets compare notes
While the 'island as Purgatory/death' idea was what I once assumed way back when with everyone else, I soon realised that it couldn't possibly be as clear cut as it seemed, what with people on the island dying, not to mention some managing to escape. I personally never liked the 'island as Purgatory' idea as it seemed quite heavy handed, and the presence of all the Others/Dharmas/Boat People just seemed to keep allowing me to reject it. As for the 'island is death' thing, I drove myself crazy asking ridiculous questions like 'but if they're already dead and the island is where their dead selves are, then how can they die more? Do they go one to some higher level of being dead?'. So I soon revised that model of thinking and over time ended up somewhere near a conclusion that was mostly supported by these final episodes.
So here's what I got from the scene where Jack is talking to his father, which is the closest we'll ever get to anay kind of proper explanation: The island really exists, on this (well the Lost universe's version of this) plane of existence, as a place with weird electro-magnetic properties either because of, or causing, the special light. It's a place that can travel through time and space and all sorts of other mind bending things, but its a real, Earthly place nonetheless. The Dharma people really were scientists who went there to study it. The smoke monster was created by the electro-magno deal and the woman who killed Jacob and his brother's real mother was from a line of people put/originating there to stop stuff like that and also what Desmond did from happening. The Others were Jacob's people who I imagine came into his service in much the same way as we saw Richard do (okay I'll admit I'm pretty vague on this part 'cause I've completely forgotten most of the more detailed stuff of the previous seasons as I suffer from mushbrain).
In this interpretation (that I'm aware I'm rambling about btw), if the island is real, it cannot be Purgatory/death. Rather, what Christian says to Jack seems to imply that what we've been calling the flash-sidewayseseses are actually Purgatory, in a sense. If we accept that the island is real (we being me), then the experiences of these characters there, no matter how truly odd, were also real. All the time traveling and that period where a few of them briefly escaped and Not Penny's Boat and the sexy time in the big cage - all happened. The original Ocianic815 passengers all crashed on that island (due to the machinations of Jacob trying to find his new candidate) and the others they gathered along the way like Miles and Daniel all actually arrived there too, 'there' being an actual location, the events that being on the island caused being events they actually experienced in their lives. Thus, they all really knew each other, in life, and so, as Christian says, they created a place to be together in death - the lives they live in the flash sidewayeseses.
Every time we saw a flash sideways, this was essentially that character in Purgatory, or whatever you want to call the place you go when you die before you move on to the actual place where you go when you die (assuming one is accepting of the notion of the 'afterlife' at all, of course). So, they all met up in the after life, and began to remember their shared history on Earth as they came into contact with one another. Obviously, they would have all died at different times, as people do, 3 examples being 1)Shannon dying like, forever ago, 2)Jack dying as we saw and 3)one of those people on that plane at the end or left on the island, Kate or Ben for example, dying some time in an unseen future. However, as Christian says, as time doesn't really exist in the flash sideways/pre-afterlife place, they all end up there together, seemingly as though their experiences there have been simultaneous (eg Shannon who died forever ago and Sayid who died not-quite-so-forever ago and Hurley who must die in the unseen future, all together in one 'moment' that isn't really a moment as time doesn't exist). Then, once they had all found each other and truly were there all together, in that church-like building (which decided to be all multi-faith in its stain glass window decor - clumsy inclusiveness, FTW!) they could go on to the actual after life part of death, as shown by Christian throwing open those doors with light streaming out of them.
Wow, I hope that makes some kind of sense.
So. If anyone is still following/caring, they may have noticed serious flaws in this, mostly due to stuff it still doesn't explain. What the hell was up with Walt? Hurley talking to dead people? Jack's (dead) dad repeatedly showing up on the island? Zombie-Sayid? Lots of other things that I can't remember right now but smarter people probably do? All I can really offer to justify these flaws is a)I'm not entirely sure of the extent to which the electro-magno powers of the island can be used to explain stuff. This
is sci-fi after all so the possibility of this is being a place that, while entirely Earthly, can bring people back/make them walk/give them powers is very present but at the same time kinda feels like a cop-out, y'know? b)stuff was just left open, without explanation, simply because they ran out of time. If we were discussing a game of skip-rope from when I was twelve, I believe this particular point would be called Interference. And finally/most likely c)I could be totally wrong, and crazy, and THAT'S why lotsa stuff still makes no sense.
I definitely feel that you're on the right track with the Biblical/generally religious elements
Hemiola (it may seem like I forgot I was replying to you and instead just started expressing my feelings in a wild fashion, but alas, this is not so), especially in terms of the uses of names like Jacob/Shepherd etc, the roles of babies/children throughout the series, references to the island as a guiding force and the debates this caused about predestination and free will, the portrayal of a young man killing his brother, and the general opposition, and often lack of clear divide, between good and evil, as well as of course direct references to the major religions in the form of Mr Eko or Richard before he got to the island, for example. However, I personally found much of this to be more on the side of allegory and metaphor than of it actually producing any kind of literal reading of the series' events in terms of an identifiable religious model. Like you say, the Jacob/Esau thing doesn't really work out in terms of what
actually happens in religious texts, but even as a half-comparison if we consider Jacob to be somewhat based on the Jacob we know from these texts, it creates a powerful image and a wonderful connection with human history, both in the religious sense and the more secular 'literary canon' sense.
So that's basically all I've got to say. Sorry. I might have exaggerated the level to which I've stopped over-thinking this show
The only thing I feel to be left seriously unexplained is that damn statue. All I got was that its missing big toe is the plug we saw Desmond pull that's keeping all the happy light in its Goonies cave (really not dropping the Goonies thing anytime soon). I think it was implied that the polar bear was from a trip the island took to the arctic at some point in its well traveled life. How it managed to survive the relocation to the tropics is a bit beyond me though. Nevertheless, it should have made a guest appearance in the final, just for kicks.
One thing I really do need to think about, if I'm going to claim that the island itself is entirely Earthly, is the appearance of dead people on the island - Many appear to Hurley, Jacob's brother sees his dead mother and Jack sees his dad. Is there some kind of pattern here? Both Jack and Hurley end up as 'gate keepers' (hey, there's another vague religious reference), and the brother ends up as Smokey, all pretty significant roles...but Jacob is also a 'gate keeper' and he doesn't get to see their mother. Seriously, these questions could go on forever.
and remember, Kate got out of the cage, too)
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Please don't think of it as "rambling"--there's no reason why your explanations/reconciliations shouldn't be as valid as anyone else's.