Thank you foggy!
I think what you have mentioned above regrading what type of data goes through WAN Accelerators and what does not,is not there in the user guide, atleast not in the 'WAN Acceleration' section. There are a few reference about Backup Repositories involvement in a Backup Copy Job
using WAN Accelerators in the 'Used Ports' section, but again they have mentioned it like the Backup Repositories (Source and Target) talks to each other only when WAN Acceleration is not used for a Backup Copy Job
Another reference Backup Repositories is in the Backup Copy Architecture
section in the User Guide for VMware vSphere, but its kind of vague and in the illustration just below it shows only the WAN Accelerator(Source) doing the data transfer. They could've atleast shown the defaults ports being used in all the diagrams in the User Guide.