OSXCross' pkg-config ignores PKG_CONFIG_* environment variables by default and maps to OSXCROSS_PKG_* to PKG_* internally to prevent including wrong header files (/usr/include, etc.).
You can restore the default behavior by setting OSXCROSS_PKG_CONFIG_USE_NATIVE_VARIABLES (env) to 1.
Usage examples:
$ x86_64-apple-darwin15-pkg-config
osxcross: warning: x86_64-apple-darwin15-pkg-config is a no-op - please see README.PKG-CONFIG.md for more
## Explanation: No MacPorts packages installed and no OSXCROSS_PKG_* variables set = no-op. ##
$ x86_64-apple-darwin15-pkg-config --libs sdl2
-L[...]/target/bin/../macports/pkgs/opt/local/lib -lSDL2
$ OSXCROSS_PKG_CONFIG_NO_MP_INC=1 x86_64-apple-darwin15-pkg-config --libs sdl2
osxcross: warning: x86_64-apple-darwin15-pkg-config is a no-op - please see README.PKG-CONFIG.md for more
$ OSXCROSS_PKG_CONFIG_LIBDIR=<path> x86_64-apple-darwin15-pkg-config
## Explanation: OSXCROSS_PKG_CONFIG_LIBDIR gets mapped to PKG_CONFIG_LIBDIR internally. ##
$ OSXCROSS_PKG_CONFIG_USE_NATIVE_VARIABLES=1 PKG_CONFIG_LIBDIR=<path> x86_64-apple-darwin15-pkg-config
## Explanation: Restores the default behavior. PKG_CONFIG_LIBDIR is used and OSXCROSS_PKG_* variables will be ignored. ##