Great questions...I've updated the help topic to (hopefully) clarify this. Short answers:
1. Only values visible in the SC UI are considered. Also, if something is low-traffic on Monday but is in reports on Tuesday, the segment will only include the Tuesday data.
2. Only values visible in the SC UI can be classified. If something gets enough traffic to be reported in the UI it can be classified from that time until the end of the month when everything resets.
In general, low-traffic values are invisible to everything except data warehouse.