This was first and foremost intended as a parody in the operatic manner, an exaggerated cartoon, you can see that in the opening scene (special edition) with the bug being spat out on a windshield. It is very clearly a staged product, any allusions to organic development long gone. Ripley is manufactured for the purposes of the mission, the opening shot in essence is of her character being unveiled as the protagonist of this operatic show. The aliens are constructed from her. The situation where they will breed is similarly staged, victims carted in.
Someone like say Verhoeven could pull this off clean through, Starship Troopers-style, gleeful, sardonic, tongue-in-cheek from beginning to end. The dissonance here is between writer, filmmaker, and lead actor, each one pulling in a different direction.
Whedon wrote a black comedy of sorts. He satirizes action heroics, masculinity, leadership (Perez and Vriess are the first to go), the military is not only inept (compared to Cameron's marines), but basically involved in shady , unethical business. He wrote what he thought would be a few memorable one-liners, to be delivered with a wink to the audience. The first part until roughly the alien breakout is closer to his idea of the film.
Enter Jeunet. He wants to do the best blockbuster money can buy, a new gamble this, the most exciting and intense firecracker toy, one of those 'big' Hollywood films that we all enthused about as teenagers and you'd have to be a joyless macaroon to say no to. He has studied a lot of Spielberg and Cameron and, daresay, meets them in equal terms. He bends Whedon's vision to his, and because he hardly spoke any English at the time, he directs actors in a perfunctory manner - some of them areonboard with Whedon's idea, others not.
And you have, quite apart from the other two, Sigourney Weaver who always felt an emotional attachment to Ripley, and who is by this point as much a shaping force as everyone else. Amidst competing visions, she insists on a heavy emotional center, which just so happens (as it did in Aliens) to emphasize a damaged personality, nightmares, schizoid tensions between motherhood and her more conventional action/hero role.
So, when this spins, it spins in three directions at once. I think it is a great joy to be able as a viewer to accommodate all three visions, you will have a helluva time I guarantee.
You will never more clearly see this rip-roaring dissonance in the Newborn being sucked out through a tiny aperture, sent out guts flying into space.
The scene is at once meant to be hilarious, gruesome, and, as you shift to Ripley's point-of-view, emotionally devastating. The scene is so appalling because it IS those three things at once, and they are simply not emotions that as humans we can easily juggle.
Jeunet was brilliantly inspired in moving the aliens underwater, this scene was a long time coming.