OpsManager documentation under "Edit a Deployment’s Configuration" mentions that changes can be made at all replica set and cluster level. However, if changes are made on the replica set or cluster level and there are members with different configuration, the following message will be displayed:

"Some processes have options inconsistent with these settings. 
Changes to options made here at the replica set level will not be applied to:"

It would be good to add information about this in: https://docs.opsmanager.mongodb.com/current/tutorial/edit-deployment/ and/or https://docs.opsmanager.mongodb.com/current/reference/deployment-advanced-options/