Is it possible to change the ownership and amend permissions on NTFS files and folders via the NetApp CLI (ONTAP 9)?
yes. it's not straightforward. but you can use two methods.
1. creating and apply a policy with "vserver security file-directory"
2. applying a GPO on the SVM AD OU that specify new permission on the path and enable it with "vserver cifs group-policy" on the filer (i think this option is more GUI friendly)