I think it's another one of those moments where Prometheus / Covenant did more damage than good. Until their release, it was accepted that it was the inside of the ship, and the scaling could be written off in the same way as seeing the scale of the Jockey when using the children actors to make it look bigger vs seeing the actual actors over its body. Now? It kind of *has* to be a structure beneath the ship, based upon the holo map of the Juggernaut in Prometheus (showing there is no such compartment) and Covenant for showing the tiny cargo hold David stands in before bombing the planet with the pathogen.
This leaves us two possibilities; either the Juggernaut is considerably smaller than the derelict on LV426 (very possible!) or we roll with the original scrip for Alien that shows that the Juggernaut is actually sitting above an underground structure (only problem with this is that, yet again, Prometheus puts a spike in that wheel- the planetoid LV426 doesn't conform with any Earth-like planet we've seen the Engineers involved in - and as seen in LV233, they have the ability to generate artificial atmospheres suitable for human life which last for (at least) thousands of years unattended, leading us to believe the derelict was a crash (Ripley confirms this, claiming in the hearing at Gateway that it was not from there).
Short version, it's the ships hold if you ignore Prometheus and Covenant (I have no problem with either of those movies, but if it came to a choice of preserving the original trilogy, I'd happily knock them to 'expanded media' category and enjoy them in the same way I do with reading Dark Horse comics) 😊👍