No, this is not a bug. The reason for this behaviour is because the settings/override/site.ini.append file has the highest priority of the configuration files. If a setting is found here, it will not even bother by checking the site access site.ini.append file.
If you want a setting different for different site accesses you should not have the variable in the override site.ini.append file
Jo Henrik Endrerud | System Developer @ Seeds Consulting | http://www.seeds.no