It should be mentioned the cryotubes are not the same variety seen in Aliens. And the colors of the Sulaco are inverted, probably for lighting reasons, the text is now white, not black on the hull. They had a bit of a continuity hiccup. It is entirely reasonable given this that "but it didn't look like the dropship hatch" they built a generic scifi set for that location. The working logic probably was, as the Queen had just removed her ovipositor recently, whatever was developing inside went KERPLUNK and found itself inside. It contained multiple eggs, though we only see one. I know it is multiple eggs, even though we see one, because Tom Woodruff Jr and Alec Gillis mentioned in an interview on this site they tested 2-3 eggs. The Assembly Cut they found was a WIP so they were playing around with the number in an error of editing.
So in short
Queen rips off a majority of her goochie
Queen still has developing Ova in her inner goochie
Queen is in landing leg.
Queen deposits eggs in the wait to get to the Sulaco.
Rips Bishop in half yada yada "Get away from her you bitch"
They go to hypersleep.
They awake in a movie with a set of continuinty problems and an editing problem
But what happened was the eggs hatched we do not see because this was a WIP cut, one regular bleeds after it cracks Newt's cryotube.
Another, a Queen facehugger, impregnates Ripley.
We know the omitted scene that made things come full circle they ran out of time and money for was all the EEVs ejecting and one either not descending fast enough or orbiting the Sulaco, and hits the Sulaco, ripping a hole in it causing a massive explosion and decompression that sends our beloved characters careening, the lifeboat hopelessly spinning out of control.
It crashes on Fury 161
The queen facehugger impregnates two to protect the queen, so it attaches itself to Babe. The Runner is born. Perhaps the third mentioned being tested by Woodruff and Gillis was for the dog. We don't know, but I think that's safe to assume. Regardless of what happened on set and the continuity errors
This was bottom line what was meant to happen.