The automation variables are deprecated, but they still work like they did before. It is recommended to use the runtime parameters, but you are not forced to do so.
In your data mapping configuration, your automation variables are automatically transferred to the Parameters tab (if you don’t see it, go to the Window menu, and select the Show View > Parameters.).
The runtime parameter will have the same name as your original automation variable (let’s call it MyVariable).
In Workflow, when you double-click on the DataMapper task, you’ll see that MyVariable automatically appears in the list of runtime parameters. This makes it a lot easier to manage the parameters required by the DM config since you see them listed in the DataMapper task, without having to open up the DM config to find out which variables are expected.