One apply action can change how a later one should behave (unfortunately).
For example: we have distcc installed and /etc/conf.d/distccd is changed. Neither of these are in the configuration.
This will happen:
- distcc gets uninstalled
/etc/conf.d/distccd gets restored to package manager state (clean file)
This is tricky without doing a second scan. As a workaround just run apply again and it will reach as "steady state".