This is what happens when building Python with conda-build (which implies doing "make install" with a custom prefix):


[...]
if test "xupgrade" != "xno"  ; then \
	case upgrade in \
		upgrade) ensurepip="--upgrade" ;; \
		install|*) ensurepip="" ;; \
	esac; \
	LD_LIBRARY_PATH=/home/antoine/miniconda3/conda-bld/work/cpython-default ./python -E -m ensurepip \
		$ensurepip --root=/ ; \
fi
Ignoring indexes: https://pypi.python.org/simple/
Requirement already up-to-date: setuptools in /home/antoine/.local/lib/python3.5/site-packages
Requirement already up-to-date: pip in /home/antoine/.local/lib/python3.5/site-packages
[...]


Note that conda-build *does* set PYTHONNOUSERSITE to make builds as isolated as possible, but the Python Makefile deliberately ignores it using "python -E"!