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It helps PR spread more evenly throughout the site and diversity of links may - I repeat, may - be a measure Google et al. use for how "natural" a set of inbound links looks.
Scenario 1: a great informational site attracts 1000 links to it over time but they are all to the homepage. Read- those 1000 links aren't natural... devalue.
Scenario 2: an average informational site attracts 500 links to it over time to all different pages within the site, less than 50% of total links are to the homepage. Read- those 500 links are natural and worth more than the 1000 in scenario 1.
You don't have to be a google phd to realise which site is credible.
That's what the tool does, shows you what proportion of links to a domain are deeplinks.