After all these years, I can just accept that the Queen planted the egg, most likely in the Dropship or possibly in the hangar.
Her eggsack was gone, but she still had one left inside her womb, or whatever you'd call it.
The location of the egg doesn't match anything seen in Aliens, but neither do the cryotubes. Those are just aesthetic differences that don't need explanation.
After hatching, the Facehugger tried to get Newt, failed, got injured, and bled acid causing the fire.
A bolt exploded and knocked a hole in Ripley's tube, allowing the hugger to get her.
This hugger, Royal or not, was capable of planting a second seed. It hitched a ride on the eev and got the dog.
And that's all there is to it. We don't need stowaway facehuggers or a compromised Bishop. It can all be taken literally; nothing in the opening sequence has to be a dream.