Seems to be a regression from PEP517 switch. Apparently, setup.py used to hardcode install paths in _config.py when `setup.py install` was used. Now we use wheels, so it instead uses sys.prefix to locate it. This breaks when venv with system site-packages is used because pkgcore tries to find its config files in the venv instead of the actual install location.
Created attachment 824903 [details, diff] pkgcore-fix-INSTALL_PREFIX.patch
Fixed with pkgcore using flit + wrapper as build backend