After a while I found what's going on in my case. Thank you everyone for comment. All of these comments were right about the safe area and its usage. But in my case the problem was in my _layout.tsx file in App directory. In this file there is located Stack by default. What caused the "double" safe area was that the first safe area was created by header of Stack. To fix this issue I simply hide this header like this:

<Stack screenOptions={{ headerShown: false }}> 

After hiding the header, the safe area that was created by me is on the right place and I can customize it.