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I have tested and agree with your findings - currently there's not a way to successfully use fixed width files that are padded with spaces in Tableau Prep. I have created an idea for such support here: https://community.tableau.com/ideas/9038 (please upvote!)
In the meantime, you might consider the possibility of first replacing the spaces with another unused character prior to importing in Tableau Prep and then replacing that character with spaces in Tableau Prep. I believe that would work. You could do this with a text editor or automate with a script.