Flynn Carson is Henry Jones III or his half brother.He and Marion may be living under an assumed name after that debacle with the Russians ("Fancies himself a swordsman"). The Ark of the Covenant was moved from Area 51 to The Library after the incident in Crystal Skull, and he never mentioned where he saw the holy grail (it was made of wood in this continuity, as well as in The Last Crusade), which may explain why he doesn't look 50 (that or he's a different son, and the father who told him stories was a stepfather, which accounts for the navy flashback much better than "costume party" or "metaphor").
Simone didn't die.When Simone finally stakes the vampire that had sired her, she felt at peace and sat with Flynn to watch the sun come up one last time, dissolving gently into dust on the wind. Yes?... But since even before the revelation of her vampirism, she's been bursting into dust clouds and reforming, over and over. It's part of her fighting style. Who's to say that she didn't simply maintain a lot more control over her dust form this time to give Flynn a romantic goodbye as she fakes her own death because she knows they cannot be together? Maybe she just doesn't want to turn him and couldn't stand to stick around to watch him die, so she left him with a dramatic farewell.
To Dracula, burying the body of one his loyal subjects was a hilarious practical joke.That's why he giggles when he explains that the body is just "A peasant in a box!" All this effort everyone has gone to, finding his body, and now dragging it to the new world and performing rituals over it with mystical artifacts. And after all that, only he knows that this is just Alistair, his favourite clothes merchant.