I have contacted Apple Support chat and they said "So it's not normal that the keyboard will leave a mark on the screen when you close it."
Also they told me to go to nearest Apple Store for inspection. They can fix it by replacing keyboard same day.
Anyone had similar experience? Is the issue really can be solved that way?
I did what they said, I bring it to Apple Store.
They said that those sign are some kind of liquid so they need to make verification that there is no liquid inside of MacBook, and if there is, no service going to be provided.
Half hour later they bring it back and confirmed that there is no liquid inside. Sadly they forgot to close two clips of back cover so they had to put it on its place by my request.
They tested keyboard and said that every button height is normal and no replacement needed.
But they can replace it for free if I wish so. Since they don't think that replacement will fix the issue I rejected replacement offer.
Overall their explanation was short, the keys are not touching the screen, when liquid appears (possibly fat from fingers), the liquid itself touches the screen. Also they said that no permanent signs should appear later, and if there will be any, they will replace the screen for free, while it is on warranty, of course.
As for me, I can see only space bar signs, but no other buttons.
So their recommendation was to clean keyboard every time before closing the lid.
Well, looks like we have to live with that.