I am no Grammarian, and if strictly grammar is what you are looking for there are some fairly eminent voices over on EL&U such as John Lawler (his CV) who would undoubtedly be able to give you an unimpeachable opinion on it.
I am not they, so I'm using Wikipedia to support my view that the use of an Imperative doesn't stop it being Second Person.
The imperative mood is used to demand or require that an action be performed. It is usually found only in the present tense, second person.
Your issue with it seems to be an interpretation of the Imperative seeming impersonal, because 'you' is not appended. However, the versions you suggest 'you focus on' rather than 'focus' would change the sense from an instruction to a description of the reader's actions, robbing the authorial voice of authority and placing the motive force with the reader.
The 'you' in an imperative is still there, it is just that it's implied.
The imperative mood is used for expressing commands, requests, and so on. So by its very nature an imperative is directly addressed to someone, and an imperative sentence typically has the second-person “you” as its implied subject.
That difference between an implied and an explicit 'you' makes a world of difference to how the verb reads. Imperatives can have an urgency and directness that the addition of 'you' can dilute.
If the section was written with 'you focus on', the narrator would just be a voice telling me what he observes me doing, rather than guiding and helping me to do it.
I tried taking the imperatives out of the passage and replacing them with 'you let', 'you focus' and 'you find':
You let the eye of your imagination be a camera...
This is the universe, a glittering ball of galaxies like the ornament on some unimaginable Christmas tree.
You find a galaxy...
You focus on the galaxy, swirled like the cream in a cup of coffee, every pinpoint of light a star.
You find a star and you focus in on its solar system, where planets barrel through the darkness around the central fires of the sun. Some planets hug close, hot enough to melt lead. Some drift far out, where the comets are born.
You find a blue planet and you focus on it. Most of it is covered in water. It's called Earth.
You find a country and you focus on it, it shows blues and greens and browns under the sun, and there's a pale oblong, which you focus on. It is an airport, a concrete hive for silver bees. There's a building there that you focus on, which is full of people and noise.
You focus on a hall inside the building full of lights and bustle, and you focus again on a bin full of rubbish, and you focus further until you see a pair of tiny eyes.You focus on them, a lot.
Masklin slid cautiously down an old burger carton
Because the verbs are now woven into more regular second person voice sentences the repetition of 'focus' loses its power and it feels as though the writer just ran out of ways to say 'look closer' and it doesn't carry us through the layers in the same way. The passage loses that cinematic zoom that takes us through space, through the layers of the atmosphere and the structure of the building itself.
In this passage, Pratchett essentially swaps his role from Narrator to Director when he tells us, the reader, to let the eye of their imagination become a camera. In that first sentence he establishes that he is talking to 'you', let the eye of your imagination become a camera. You are operating the camera, he is directing your actions, describing what you see as you follow his direction, then instructing again until we arrive at his desired level of focus, arrive at Masklin.
For myself, I've always found these passages in the Wings trilogy intensely direct, as if, with my eye as the camera and all my attention channeled down the barrel of the lens, Pratchett is speaking directly into my consciousness to make sure I frame the shot exactly as he intends.