I’ve had the same experience. Post-deployment activities for these items is almost always a one-time activity. We never deploy adapter connections with Deployer. And never automated TN components either – very little value to be gained there because they don’t change much if ever.
The intent of this is understandable. Reduce manual activity. But for these types of components, it doesn’t reduce much if any. The activity to define the substitution vars is still manual somewhere. And indeed, what this introduces is additional work in troubleshooting the automation scripts when things go wrong. Invariably, someone at some point forgets to configure the prod settings in the right place. So then there is work to figure out why the script didn’t work and recover. And depending upon the settings/activity after the “bad” deployment, the data impacts can be disastrous.
This is not to say “avoid automation in deployments.” Rather, be selective and use it when it actually provides value that offsets the potential issues. For us, there was no value in automating adapter connection pools nor TN profiles. Just spend the 5 minutes to manually define them in prod and be done with it. 
#cicd#Integration-Server-and-ESB#Deployer#Substitution#Trading-Networks#webMethods