Nowadays it's all done via Radio. The advantage is everyone can hear who's doing what and where. The disadvantage is everyone can hear who's doing what and where.
When I started as a Switchman some Foreman preferred working "quiet" because they they didn't want the yardmaster monitoring every move they made. They also didn't trust the radio because they didn't have them when they started and were used to working without them. In the days before radios crews developed some elaborate hand signs to communicate, which went way beyond the basic ones listed in the book of rules. It bigger yards a guy might even be required to "pass" signs to the engineer. That might have been what the guy on the boxcar roof was doing.
Nowadays most new hires know hand signals but stick with the radio.