You can use the data from nuitrack.UserFrame (see the script SegmentPaint.cs), where each element of the array is the user id.
More details: http://download.3divi.com/Nuitrack/doc/classnuitrack_1_1UserFrame.html
Knowing that, you can separate the interaction of objects through layers or tags at the Unity level.
You can use our tutorial for reference: http://download.3divi.com/Nuitrack/doc/UnitySegment_page.html
For your case, you need to modify the UpdateFrame method in the GameColliders.cs script so that colliderObjects [c, r] receives a tag, a layer or any other identifying parameter according to the userId for the current pixel.