Small intro, Node.js is written in C++ and JS engine V8 is written in the C++ too, so when people say native something in Node.js they usually mean C++ stuff that can be called from the JS code or not and etc.
In that particular case native_context is just the object that stores some fields from the Native side of the Node.js. Even datatypes are C++ entities under the hood and you are operating with these “native” entities.
There is no way you can change or modify the native_context because this thing is defined during the build of the Node.js executable and defined in the C++ code. You can dig up more about these in the Node.js repository in C++ source code if you want to know more about that.
https://github.com/nodejs/node
UPD: You can search it in the code e.g. here is what you can find, but you need to know some C++ to understand.
