In what application are you running
See the sample projects on Twixtor Support Page on the website
The tracking points serve the same purpose as the Splines, basically help Twixtor in certain circumstances (when it does not work well). Imagine something crosses the screen in 5 frames, it’s way out of reach of the internal tracking, so if you animate points that follow the image content for these 5 frames, then Twixtor should work much better…
In AE for example you can’t attach a tracker to a roto mask control point, so if you track some points, it will guide Twixtor to start somewhere internally. In Combustion since you can attach a tracker to a roto mask shape then the points are not necessarily useful. In other applications, there is no way for us to support roto masks (like there is no such things in FCP), so you can always use individual points.
Pierre