Just offering up my own personal theories as a fan of the show. Don't take it as gospel.
What was the point of showing the island under water in LA X?
Perhaps it symbolized that Jack and the other castmates were no longer aware of the island. Or it could just be, since everything in the sideways world was a little bit different than it was in real life, that the island was submerged in purgatory.
What was the deal with David (Jacks's son in the sideways)? Was he completely imaginary?
He was. I really feel strongly that the point of the David character was to benefit Jack and help him draw closure. His relationship to David, at least in the beginning, was exactly like his relationship with his own father. It was fractured and looked beyond repair. But Jack differed from Christian because he ultimately reached out to his own son and repaired their bond. This was part of Jack's redemption. In order to forgive his father, gain island realization, and move on, he had to first understand what it was that his father went through with him. The David character helped repair the side of Jack that he never thought could be repaired.
Why was Penny in the church, but not Daniel or Eloise?
I've talked with other people about who was left out and who was put in to the final scene at the church. I chalk a lot of it up to certain characters being too minor to include. Jack didn't really have a special relationship with Eloise or Daniel. The people in the church were mostly those who were closest to him. True, he didn't have a relationship with Penny, either, but she was there for the whole "couples reunion" bit.
Why didn't Jack (on the island) get overcome by the EM after he recorked the hole? Why didn't he turn into a Smoke Monster?
Jack was the island guardian when he decided to go down the hole, even if he did give the job to Hurly prior to actually going down the hole. Jack gets to write his own rules as a result.
Was Widmore lying about having the plane booby trapped with more explosives? Who was the source of the original bomb, Widmore or Flocke?
Not entirely sure, but it certainly didn't bother Fake Locke that the bombs were there. It helped him with his con.
Did we ever see Boone have his revelation?
No, but then again Boone is busy with the "Vampire Diaries". Weak explanation, but it's probably true.
Why did Kate change her clothes at the church?
I noticed that, too. I'm really not sure what the significance of that was.
Why wasn't Richard at the church?
I still think that the church would have been super crowded had everyone been in there. And secondly, this was about Jack. Jack wasn't very involved with Alpert throughout the show.