Installing Python with prefix that equals "/" seems to not install the dymic libraries like _collections. The steps I performed to install it:

./configure --prefix=/ \
        --with-threads \
        --enable-shared \
        --enable-ipv6 \
        --with-system-ffi \
        --with-system-expat
make
make install

I saw that during the installation that the sharedinstall rule from Makefile.pre (originally defined in Makefile.pre.in) fails to remove $(DESTDIR)$(DESTSHARED)/_sysconfigdata.py* so I manually created the leading directory and touched the file it was looking for (I could've modified Makefile.pre too) and it actually worked - lib-dynload was created and the .so files where installed in it.

I have tried using empty string as prefix but that causes runtime issues since - Python is not able to find the site-packages directory.

Cheers!