You quoted what I was going to reference in my answer already! This seems to me like a perfect example of Lampshade Hanging which is :

the writers' trick of dealing with any element of the story that threatens the audience's Willing Suspension of Disbelief, whether a very implausible plot development, or a particularly blatant use of a trope, by calling attention to it and simply moving on.

You quoted what I was going to reference in my answer already! This seems to me like a perfect example of Lampshade Hanging which is :

the writers' trick of dealing with any element of the story that threatens the audience's Willing Suspension of Disbelief, whether a very implausible plot development, or a particularly blatant use of a trope, by calling attention to it and simply moving on.

As to what the aliens could have done they could have beamed all the nitrogen out of the humans (and mouse!) They would also have to beam out some of the other pressurized gasses. Probably a little bit at a time as they brought everyone up. They did show themselves to have a higher level of technology than we have (example the control of water when providing a room for Virgil to breath in).

I don't know if they used "beaming" technology, and have nothing to back that up, but it is possible which is what the question asks. :)

You quoted what I was going to reference in my answer already! This seems to me like a perfect example of Lampshade Hanging which is :

the writers' trick of dealing with any element of the story that threatens the audience's Willing Suspension of Disbelief, whether a very implausible plot development, or a particularly blatant use of a trope, by calling attention to it and simply moving on.

As to what the aliens could have done they could have beamed all the nitrogen out of the humans (and mouse!) They would also have to beam out some of the other pressurized gasses. Probably a little bit at a time as they brought everyone up. They did show themselves to have a higher level of technology than we have (example the control of water when providing a room for Virgil to breath in).

I don't know if they used "beaming" technology, and have nothing to back that up, but it is possible which is what the question asks. :)

You quoted what I was going to reference in my answer already! This seems to me like a perfect example of Lampshade Hanging which is :

the writers' trick of dealing with any element of the story that threatens the audience's Willing Suspension of Disbelief, whether a very implausible plot development, or a particularly blatant use of a trope, by calling attention to it and simply moving on.