That's one of the things I really disliked actually - because they messed up the last act's structure for it.
The audience knows they switched (and Danny would know as well if she had checked for the wound she inflicted with the necklace).
Yet, the movie pretends the audience does not know and barfs out the last act with a random fully grown Alien suddenly being on the ship. I mean, of course it is but it's sudden appearance is so stupid. Simply because they can't show David implanting the Alien etc. - because they don't want to reveal the "twist" lol
Ideally they should have included the switch (but make it less obvious) but show how an Alien gained access to the ship on its own.
Edit: and while we are at it. I don't get why they didn't introduce the final Alien in the shower scene instead of a computer warning. Start with the sex scene and then bam, Alien. Don't even need to reshoot the scene to get a nice surprise (if it wasn't already in the trailer

).