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You can do this by adding a text input with that column and then a union that on to the data.
There is other ways, one being the Ensure Fields Tool in the CReW Macro Pack, and another using a Field Info tool to get a list of the fields that exist and comparing against a list, but the text input is quick and solves the problem.
Note: To quickly get a text input with all the fields required, look at the browse on a sample of the data that has all the fields, highlight the first row, press the copy icon and 'Selected Cells with Headers', then right click on the canvas and paste, then you can just delete that row in the text input.
Using an append tool, you will get a duplicate column if the column already exists. As you said, you can't use a Join tool, but a Union tool will stack rather than joining and so you will just get the extra column if it doesn't exist.