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Say the bot is indexing an external site and comes accross a link to my site and my external urls have a refrerer in the url for tracking which is removed with a 301. Does Google actually follow the link and pick up the 301 and hence index or log a link to the correct page or just log the url, give the destination page a new id and then a potential duplicate content issue?
The way you are handling those tracking query strings sounds quite well thought out. And as long as there is only one 301 redirect, and not a chain of two or more, then the backlink influence will pass through the redirect to the url without the query string.