Yes, it is compatible, but the setup can't be done directly on prefabs anymore.
Use this solution:
1. Make a duplicate of your character before making it a ragdoll or drag in a fresh instance of the model
2. Use BipedRagdollCreator on the duplicate to make it a ragdoll.
3. Add PuppetMaster to the ragdoll.
4. Assign the original character as "Target Root" in PuppetMaster.
5. Click on "Set Up PuppetMaster".
So if Target Root is not the same gameobject as PuppetMaster, it will not have to duplicate the character and remove any unnecessary components from the duplicate, which is not allowed anymore for prefabs in Unity 2018.3.