"When installing a python package that has `headers`, these headers are usually installed under the main python include directory".  Can you give some specific examples of packages and platforms where that is the case?  Just taking a quick look at some packages I happen to have installed, like lxml and cffi using a vanilla pip with a vanilla Unix-y Python 3.5.1, their header files get installed in the site-packages directory by default (using pip), not the main Python include directory.  And various distributors of Python have their own preferences where to install things, for example, the locations you cite are those used by Homebrew on OS X and differ from other OS X Pythons.  I'm not sure that there is a general solution as things stand now; I think there is probably a lot of variability among packages (e.g. their setup.py) and Python distributions.