The part in the reference guide you are referring to is specifically about Java in the Cloud. My suspicion is that the propertypermissions in the modeler aren't in sync with de default permissions in the cloud.
You can add the property permission yourself in the policy file which is located in the runtime folder at the location where the business modeler is installed. Opposed to 4.5.x and earlier, in 4.6.0 a lot of propertypermissions are set in the policy file.
You can find more info about this policy file here.