Hello,
The extraOptions option adds extra parameters to the soffice command. If the UserInstallation was being added in the phpdocxconfig.ini file, extraOptions is added at the end of the command, so only the first UserInstallation parameter is readed by LibreOffice. In this case, the best approach is removing UserInstallation from the phpdocxconfig.ini and add a custom one using PHP.
Regards.