If you are developing a library, MonoDevelop can automatically generate a .pc file for your project
(in the project options dialog, select “Linux Deployment Settings”, and check the “Generate .pc file” option).
which part of Makefile.include installs the .pc files?
not everything uses that Makefile.include
that is what MonoDevelop auto-generate
with the LINUX_PKGCONFIG var
so patching the path in that include file should do the trick