Bishop doesn't say "Burke ORDERED me to prepare the specimens for return to company labs". He says he "instructed". Instructed and ordered aren't the same thing!!!
If I give you instructions on how to do something or I suggest how you should do something "instruct" that doesn't mean I'm ordering you to do it!
And all of that's irrelevant anyway. The point we've all made hundreds of times is the Marines (who were in charge of the operation, NOT WY) were preoccupied and did not give their input on the facehuggers being transported.
The point is Burke has gone around them, he hasn't asked Gorman or Hicks if he can transport the specimens, he's gone straight to Bishop because Bishop is programed to take instructions from humans. Burke has done this on purpose as he knows the chain of command within the Marines is fractured, he knows they ate stressed out and preoccupied with other matters. He does this AFTER half of the Marines are killed or incapacity in the nest, NOT before when everyone is calm and level headed. How are you not understanding that? Had Bishop been WY property and had Bishop been under Burkes command, Burke would have 'ordered' him to secure the specimens the moment they discovered them, not 4 hours later when they've lost half their Marines, the APC and their only way off the colony. Why wouldn't he have transported the specimens to the dropship immediately? Ferro and co weren't doing anything at the time they had been ordered to touch down and await instructions! They could have helped Bishop move the specimens on board!
Because Burke has NO authority that's why! And the movie makes that clear! The only time Burke realises he might get away with collecting the specimens is when all chaos has broken loose!
Now had Bishop prepared the specimens for transport before Ripley had got to him and told him to destroy them, there is absolutely no doubt any of the Marines would have allowed it. Hicks wouldn't have gone with it, Hudson certainly wouldn't have, Vasquez absolutely wouldn't have accepted it, Gorman regardless of his stance would have likely sided with Hicks due to not wanting to rock the boat anymore due to his previous errors of judgement. The specimens would never have got off planet while any of those Marines were aware of it and the point is Burke was trying to do it while they WERENT aware. How does that say Burke is in charge of Bishop, can order him around and has any authority. It says the exact opposite.
Let's also use this fool proof logic that WY is NOT after the Alien in Aliens and that they don't believe Ripley. Hence Burke can't possibly be working with any higher up WY officials while on LV-426.
This is because:
You think WY absolutely knows about the Alien and wants live specimens desperately during the events of Aliens? You're incorrect. If I want these specimens, I believe they exist and I'm desperate to get my hands on some' do I go to a colony of 156 people that's been infected and go have my pick of the organisms there? Yes of course I would that's absolutely my best chance of getting hold of some.
Or do I wait until most of said specimens have been destroyed by a nuclear blast and then go chasing after one single specimen on a prison planet? No that would be logically stupid!
Oh it's because I haven't believed Ripley and her story! I think she's nuts! I don't believe these aliens exist so let the Colonial Marines waste their time and resources going to investigate a 'downed transmitter'.
The only time I realise I've been mistaken is suddenly I've intercepted a transmission from the Sulaco saying an extra terrestrial organism has caused a cryo tube fire and has been ejected along with Ripley down to Fury 161. Ahhh Ripley was telling the truth, right let's immediately dispatch our OWN WY ship and go get it.
All proof that WY isn't being sinister during Aliens, they simply don't believe Ripley. Otherwise they would have immediately gone themselves to the Colony. So no Burke isn't taking sinister behind the scenes orders, no he's not in charge of Bishop, no WY isn't in on the events of the colony, no WY doesn't at that point believe Xenomorphs are real, no WY doesn't believe Ripley. They only suddenly do realise once the Sulaco has ejected its EEV and the ships sensor readings are broadcast back to them! Not before, not ONE minute before that!
So your theories are nonsense. Burke during the events of Aliens is just single handedly trying to seize an opportunity, for himself and only himself.