Well, after testing the tool on a few sites (Including my own) I have come to the conclusion that while it may not be a very accurate tool, it ONLY counts Backlinks that are mathematically calculated as ORGANIC in Google.
From a previous answer I provided on another thread:
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Organic relevant links Vs. Spammy Irrelevant links - The algorithm tries to calculate the relevance of the source of the link Vs. the destination. If the sources content is similar / relevant / reputable / & on a page with a Very low amount of other external links, it will be labeled Organic (In theory). Spammy links won't get listed in a backlink report, Don't worry though, they are still there, you can type your Exact URL in the search engine & if it shows up, you ARE indexed. Then click on the cached or extended report for the ones not shown. You will find that allot of the backlinks ARE listed there.
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Hope this helped!