Here is an alternative theory to try to cover the eternal plothole (yes another one, I don't claim to hold the truth and my apologies if I disturb anyone
) :
After Bishop was ripped into 2, the lower part of his body got eggmorphed. How can that be possible ?
First of all, it is just an assumption, but the egg seems smaller than "Brett's egg" and "Dallas egg " ( I assume the letters of S.U.L.A.C.O. are smaller than a human head) and the texture of "the Sulaco Egg" does not look the same.
An explanation could be that just half a body is used to make an egg and its different appearance is perhaps because Bishop is an android (of course, the most important thing is that the egg is viable over the appearance)
As a reminder, we don't know all the capabilities of the Alien and its lifecycle, not to mention the Queen. Scott said that Ash was 2/3 human. Bishop is a more recent model of android and is probably closer than that (although the inside of the body does not look too human with tubes etc). Has he got some kind of cells for some parts of his body, has he got DNA or not, and does the Alien absolutely need a lifeform with DNA to make an egg ? We don't know (or I missed something ?). He is maybe not a viable host for a facehugger but still could be cocooned. It is possible that the eggs found in the derelict came from a biomechanoid specie, if they were cocooned, why not a "synthetic" ?
How could he get eggmorphed provided that the Queen barely touches him before he gets halved ? The fact of being pierced by the tail might be sufficient but then why only the lower part got cocooned ? Remember when we see acid (only acid ?) driping near Bishop's shoe. This liquid could have been spread on the legs before he was cut off. Of course we were not focused on this but rather on the fact of him being lifted so high. This liquid could be part of the eggmorphing process.
Up to now, we know that Brett and Dallas were changed into an egg and they were put above ground, it means there must be sticky matter on them in order to do so. Maybe she put on him that sticky stuff with the little arms before ripping him off ? Or that liquid has also got some sticky proprieties ?
The Queen has such power that the legs flew quite far away (near the Airway "E3 D") and they could have landed and sticked above the ground on the location seen in the opening of A3. Around the egg, nothing which could suggest a lair, a hive, (like when Ripley locates her two cocooned partners before escaping in the Narcissus), because the Queen had no time to do her job.
What about the vacuum, was that "Alien glue" strong enough to counter it ? Or maybe the legs got stucked physically speaking ? Or both ?
As it was already said, considering Bishop and Ripley would scan and search every inch of he dropship and the Sulaco for any more aliens onboard, they possibly didn't think the legs got impregnated which is of course a mistake (this early stage of cocooned legs could have not been detected by the scan).
Just before hypersleep, Bishop is wrapped and I believe intestine tubes were too (the sort of aluminium foil on the location of the legs would be there to protect the intestine tubes)
In A3, when Ripley wants answers from him and takes the upper body, we don't see at all the lower part next to it..
In this theory, unfortunately there are many "maybe" or "could" , but please just don't tell me that in the novelization, they threw the legs into the trashcan of the Sulaco
