I've recently moved /etc/python-exec/python-exec.conf from dev-lang/python-exec to dev-lang/python-exec-conf, and changed the installed default from empty-ish file to the current PYTHON_TARGETS. My assumption were that users who had changed the file (either directly or via eselect-python) would have the changes confirmed via CONFIG_PROTECT. However, Polynomial-C reports that CONFIG_PROTECT fired only on some of his machines, while on others Portage silently replaced his config with a new one. Zac, any idea what might be happening there?
The only scenario that I'm aware of is triggered when /etc/python-exec/python-exec.conf had been installed by a binary package created with quickpkg --include-config=y. Then FEATURES=config-protect-if-modified sees the file as unprotected, and therefore it is simply overwritten.