Settings in the two configuration parameter defaults files are recognized even when they have been commented out, because the conversion script that reads these files doesn't discard comment lines before looking for value settings. If multiple settings for the same parameter appear, the last one present will be used.
This problem is especially apparent for the EPICS_TIMEZONE variable, which has four separate lines defining it in the CONFIG_SITE_ENV file, although only the third one is not commented out. Sites that just edit the uncommented entry without removing the fourth one will find their IOCs default to BESSY's timezone.
The IP address of a site's NTP time server cannot be set in the CONFIG_SITE_ENV file and then used automatically by all IOCs; In R3.14.5 this information must be set in an environment variable from the IOC's st.cmd file before iocInit.