I've been using a policy that runs at "Recurring Check-In," "Once per user per computer" instead of a Configuration Profile or a script to set default Docks for my different departments.
The pre-work is to load all your app Dock icons into Jamf Admin first. By this I mean all the default Apple Dock apps, and the apps you want to install. I started by capturing all the Dock icons from a standard out of the box Mac into Jamf Pro. Then, install the third-party apps and capture those Dock icons.
When you create the policy, you can then set it to first remove any default Dock icons you want, and then add the new ones in the order that you want them to appear. You can create different policies scoped for different computer groups by just cloning your initial Dock policy, and then customize it for the next computer group and scope it appropriately. I work for a marketing company, so my Accounts folks don't get the same apps, and therefore the same Dock icons, as those in Creative or Production depts.
The policy can be set to run after you have installed the appropriate software for the scoped computer.
This effectively has the same functionality as the old Workgroup Manager option for setting the Dock "Once." The Dock is then free to be manipulated by the end user, but at least you have provided the aliases to your standard apps and removed the ones they won't use.
The other nice thing about running it as a policy is that you can also have it run scripts for other default settings. For example, I have it run scripts that set Dock behavior, Finder preferences, Launch Services defaults, and Spotlight settings.
Please see my screen shot as a basic example.
