Hi,
One main reason is that the Application Summary report shows all the calls that have been managed by an Application, all type of calls: answered, abandoned before queued, abandoned in queue, queued, dequeued, etc.
The CSQ report show all the calls that have been send to a specific CSQ, and, for example it doesn't count calls abandoned before queued on the CSQ. You can send calls to a CSQ from different applications, too.
Hope this helps,
Juan Luis