It looks to me like the first parameter passed to the shiny-server binary is interpreted as the config file. /etc/shiny-server/shiny-server.conf is just the default.
$ /opt/shiny-server/bin/shiny-server /home/cole/shiny-server.conf
[2018-12-11 17:04:29.302] [INFO] shiny-server - Shiny Server (Commercial) v1.5.1.760 (Node.js v6.9.1)
[2018-12-11 17:04:29.305] [INFO] shiny-server - Using config file "/home/cole/shiny-server.conf"
[2018-12-11 17:04:29.347] [ERROR] shiny-server - Error loading config: File "/home/cole/shiny-server.conf" does not exist