Hi @jfg1306 ,
There is currently not a way to automatically run CLI scripts, but I always thought it would be a cool feature so if you feel strongly about it please request it via support 
As it stands, two common options for configuration are triggering the scripts as you have noted, or using SEMP to perform your configuration. Either way Iād recommend a SEMP call before executing either to check that the container is up and running 