If less than all of a carrier's fares are available in the GDS, you are certainly not getting full content. Whether that excuses you from having to pay the GDS's fee depends on the exact language of your GDS contract.
This GDS vendor fee appears here to stay: Travel Weekly travelweekly.com - get the latest breaking news, showbiz & celebrity photos, sport news & rumours, viral videos and top stories from travelweekly.com Daily Mail and Mail on Sunday newspapers.