To be fair, we reworked the OVA image completely between the 2.x and the 3.x branch - that is the reason they behave different.
I have created an issue for the documentation to have that visible: https://github.com/Graylog2/documentation/issues/526
@Totally_Not_A_Robot graylog-ctl is dead as it creates more problems than it solves.
@harryw the documentation for 3.0 will be “on-point” with the release, we have entered now the code freeze for 3.0 and concentrate on testing, bug fixes and documentation.