I'll offer some possibilties:
"What was the point of showing the island under water in LA X?"
I think that shot was a flash forward to the end of this season. We did see many chunks of the island falling in the ocean when Desmond uncorked hell. Maybe the whole side that we saw had indeed sunk.
Anther possibility is that the sunken island was pictured as a possible parallel universe if Jack had failed.
"What was the deal with David (Jacks's son in the sideways)? Was he completely imaginary?"
As I wrote elsewhere, Jack needed closure so he probably dreamt him, to show himself he could be a good dad and to understand his own father. That's what I think the whole FS were: Dreams. As such, they didn't need to make sense.
"Why was Penny in the church, but not Daniel or Eloise?"
The island gave Desmond back to Penny. Eloise asked Desmond not to bring Daniel immediately because she wanted to spend more time with the son that the island took away from her.
"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?"
First, I'd like to point out we don't know anything about what happened on the island after Jack recorked hell. There could be another smoke monster that would become Hurley's problem.
I don't believe that. As I mentioned somewhere else, I think MIB made a deal with the devil at the moment of his death: He'd do everything to turn off the light if he could get his humanity back. That's why Locke stopped being Smokey once the light was off: The devil respected his pact. Jack simply didn't make that deal but accepted his own death. Death by EM forces doesn't have to be immediate, especially since Jack entered the cave with the field down. Jack did die soon after.
"Why wasn't Richard at the church?"
The people important to Richard would be reunited in another "church".
Are the other questions really important?