Rebase ports are used in RA/NFA to redirect traffic that is destined for a port that happens to be a destination port for a configured application mapping. Here is an example:
I create an application mapping that redirects my video conferencing traffic which happens to be on a range of ports from 3260-3265 over TCP and I decide to redirect that to port 62000. I have confirmed initially that port 62000 has not seen any traffic.
Now suppose I start to see traffic on port 62000. Since that port is already in use for my application mapping, RA will send the traffic directly destined for 62000 to port 9000 (the default port defined in Application Settings for the TCP Rebase Port) as to not have it added into the mapped traffic.
It should be noted that the rebase port can be thought of as a bucket, so if there are multiple conflicts with application mappings you will see a range of ports ending up being identified with the appropriate rebase port.