How pkg-config decides which look up path to add by default?

I'm trying to run pkg-config on my 64bits elementary (ubuntu 14.04) from a .net gui application and it says that it doesn't find my packages that are found when I run the exact command from a terminal.

For reference, here's the command:

pkg-config --cflags --libs  glib-2.0 gobject-2.0

Using the PKG_CONFIG_DEBUG_SPEW I managed to get detailed debug info for pkg-config and it looks like it initializes itself differently in the two cases.

Initialization in terminal:

Adding directory '/usr/share/pkgconfig' from PKG_CONFIG_PATH
Adding directory '/usr/lib/pkgconfig' from PKG_CONFIG_PATH

Initialization in .net gui application

Adding directory '/usr/local/lib/x86_64-linux-gnu/pkgconfig' from PKG_CONFIG_PATH
Adding directory '/usr/local/lib/pkgconfig' from PKG_CONFIG_PATH
Adding directory '/usr/local/share/pkgconfig' from PKG_CONFIG_PATH
Adding directory '/usr/lib/x86_64-linux-gnu/pkgconfig' from PKG_CONFIG_PATH
Adding directory '/usr/lib/pkgconfig' from PKG_CONFIG_PATH
Adding directory '/usr/share/pkgconfig' from PKG_CONFIG_PATH

Of course my libraries are defined in the missing directory.

Why are the two initializations different?

How can I tell pkg-config to initialize the same it does in the terminal?

Note: I know that I can set the PKG_CONFIG_PATH before calling pkg-config but I would prefer a simpler solution if available.