I think that automatic means that you can get a job in the lowest playable league; so if you're only playing with First Divisions, with automatic reputation, you're still going to have a high reputation. However, if you are loading all the leagues from a country, automatic is the best/most realistic to go for because it gives you the reputation to manage at the lowest level.
I think having automatic reputation also means that your reputation will change with your club's reputation, so going from, say England to, say, Basingstoke, all of a sudden nobody will have hear of you.
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