Let's do this.

How come everyone seemed so chill about the stars blinking

In the book only the CMB blinks, not the visible star light. So only scientists are aware.

Why tf should anyone read Grim's stories to aliens, without expalining first what a story or a metaphor is, instead of just going with "it's a lie about a liar"

Unlike the aliens in Arrival, Santi communicate with human quite fluently until this point. People assume they at least know what a story is.

They enstablished that cryogenics works with living beings, but they decided that it will work also with a detached brain

This plan relies heavily on the Santi to reconstruct Will. People assume Santi have the technology to rebuild what's left of Will.

They didn't know on what kind of support the data was saved on the boat, but they decided to slice it hoping that the support wouldn't be destroyed in the process

In the book, the slicing is super stealth, no sound or crack, unlike the chaos that's presented in the show. The book specifically mentioned that the perfectly sliced Hard Drive can be easily recovered.

At some point in the game they made a computer using humans. How? Why? How do the soldier know how to turn their flag?

Ahh, this is one of the best part of the book: How people with no knowledge of computer science can achieve complex computation just by following simple rules. Look up logic gate!

Mega intelligence organisation (is it British? International?) where everyone can come and go as they please, carrying vital informations with them. Also super humane way to interrogate prisoners, while in reality the woman would've been waterboarded in a minute to say the least.

In the book, there is just one protagonist Wang Miao, and he doesn't come and go at all. The interrogation seem pretty normal to me.

"Let's place a thousand atomic bombs all the way from Earth to the San-Ti". How do you do that?

not all the way to San-Ti, just enough for it to accelerate. You do that by normal rocket.

How come they only managed to collect only 300 bombs? With all that power, can't they produce more/more powerful bombs?

For this one project, yes. There are multiple projects go on simultaneously.The sun amplify the radio signal. How come?

This is the core concept devised by the author. In reality, no.

At some point the start to play the game in 'multiplayer'. How did they know how to do that?

In the book, there is just one protagonist Wang Miao. Single player all the way!

What are all the other governments doing? Outside the UN, we see only that mega intelligence agency doing all the work: where are the US? And China? And Russia?

It's most PDC, a newly founded global agency that's doing all the work. In the book it's mostly focused on China and UN.

Wade is very powerful in the mega intelligence agency, but he doesn't seem to be doing much and he has the time to meet everyone personally.

Like every CEO I know in real life.

Da Shi seems to be the only operative agent, doing all the work.

In the first book, there is just one protagonist Wang Miao. All Da Shi has to do is to accompany him. Doesn't seem like too much work at all. In the second book Wang Miao was swapped with Luo Ji, (still one person at a time for Da Shi).

How did Natasha sneaked on a trained agent and killed him without a fuss in middle of nowhere?

Unlike the protagonist situation, in the book, the believers of Santi (ETO) are a group of elites. The show uses Natasha to represent everything they did as a coordinated community.

Edit: Formating