s.linkInternalFilters: The linkInternalFilters variable within the s_code.js file is used in exit link tracking. If s.trackExternalLinks is set to true, it is used to determine if a specific link a visitor clicked is internal to your organization's site or not. Clicked links that match a value in s.linkInternalFilters are ignored. And, links that don't match any values are sent to SiteCatalyst as an exit link.
Internal URL Filters: The Internal URL filters within the Admin Console are used in Traffic Sources reports, such as the Referring Domain report. Every s.t() request checks to see if the referring URL (contained within the referrer variable) matches any of the rules. Referring URLs that match any of these rules are excluded from all Traffic Sources reports, while referring URLs that do not are included.
Adobe recommends that s.linkInternalFilters and Internal URL filters match each other. However, the two operate independently and serve separate functions.