I found this great documentation which entails the discrepancies and differences in the UCCX reporting for similar constructs like Calls Handles, Abandoned, RNA etc.
One classical case in point is when you run the Historical reports to get Abandoned Call data from CSQ Summary Report versus Application Summary reports. The Application Summary report will also reflect the calls which were transferred lets say top VM and set as Handled in the Script using SetContactInfo step. Hence you will see that Application Summary reports will generally show more Abandoned Calls than CSQ Summary reports. You will see the same anomaly in the Call Presented metric when you run these two reports.