As of 4.8 Preview 3 and possibly earlier, packaging a blueprint only project with Paper2D and LeapMotionController disabled results in CDO errors for those plugins.
This is related to Error: CDO Constructor Failed to find long list of engine and paper 2d components - Blueprint - Unreal Engine Forums and https://answers.unrealengine.com/questions/174942/android-error-cd0-constructor-umgpaper2d-files.html but I don’t believe this is Android specific anymore. Neither question seems to address this explicit issue of disabling plugins on Win64, sorry in advance if this is seen as a duplicate.
This is easily reproducible in packaging a brand new Blueprint only project with these plugins disabled on Win64. It seems like these plugins are being compiled into the main engine binary but don’t respect themselves being disabled?