The behavior you are seeing is actually intended. The Copy Features tool has an optional configuration keyword parameter, which you only see if you expand the ArcSDE settings option on the tool dialog. When the tool is used from a desktop application, such as ArcMap, teh default value of this parameter is set to the configuration keyword in the environment settings. This behavior is not seen from a standalone script, as there is no parent application with an environment.
Within the script, expressly set the configuration setting to nothing so that any value passed from the application is not used when a tool is run within the script, as below, or make sure the setting is not set in the calling appllication.
gp.CopyFeatures_management(input, output, "", "0", "0", "0")
# Reset the config keyword to nothing
gp.configkeyword = ""