Single #include pulls in all libraries
What you are experiencing is due to the fact that your use case does not match with the Arduino foreseen use cases of "importing a library".  

Basically you want the use case "include a file" and you get "import a library". The use case "import file" is simply not foreseen in the Arduino IDE.
Because the Arduino IDE add the library to your code it also adds the source doe files to your code. When these source codes contain global variables (which is very common and not a bad practise in embedded world) these will be part of your final code. As such your sketch will increase size even if you do not use these global variables.  

To answer questions
1) yes it is normal because the use case "include file" is translated into "include library" in .ino files in the Arduino IDE.
Why this does not happen for the core? The core is first linked into a archive and then linked to the sketch. This leaves the linker more options to remove stuff.

2) I think the easiest is to copy the pins.h file in your sketch work folder (and you probably will need to restart the Arduino IDE).
Another option is to go for a real IDE like the arduino eclipse plugin called sloeber (which I develop)
In sloeber you could link to the pins.h file instead of copying. You could also reference the pins.h with a (partial/full) path avoinding the library include.

3) All global variables, static and similar stuff in the source code of the "imported libraries"