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We had a similar situation and a Moz rep (thanks Samantha) pointed out in the Help material (very close to what she wrote in the earlier post) about the 90% figure. We realized the reason for the message -  because the affected pages had very little content and the page header section and the page footer section (word press site) dominated the page content. We realized the issue could be ignored in our case.

The only real problem is disavowing a site that might be helping you, but in this case that doesn't seem likely. It's more about a waste of your time and efforts.