When you're working with Pass-through Zones in an O-D project, and you examine O-D pairs where the Origin and Destination Zones are the same, then the O-D StL Index is actually the same as the Zone Activity Index for the given Zone. In your .csv downloads, you should be able to see that the O-D Traffic, Origin Zone Traffic and Destination Traffic Indexes are all the same values.
This means that when the Origins and Destinations are the same, the StL Index represents the total volume of trips that pass through the Zone, regardless of where those trips start and end. For this reason, these StL Index values are likely going to be much higher as compared to those where the the Origins and Destinations are different. You may want to exclude these intrazonal O-D pairs from your analysis.