What makes you believe that flexvol is not supported?
What I see in NBU for NDMP manual: https://www.veritas.com/support/en_US/doc/24427212-130506194-0/v108973812-130506194
NetBackup recommends that a NetApp cDOT cluster run in SVM-scoped NDMP mode (also called Vserver aware mode).
NetBackup supports optimal backup, restore, and duplication of NetApp cDOT FlexVol volumes using the CAB extension. The NetApp cDOT server (that runs in Vserver aware mode) provides unique location information (affinity) about volumes and tape drives. Using this affinity information, NetBackup performs a local backup instead of a three-way or remote backup if a volume and a tape drive share the same affinity. If multiple volumes that are hosted on different nodes are backed up or restored using the same job, NetBackup may switch drive paths if necessary (and possible) to perform the local backup.
For Accelerator to work, the only requirement is that the backup must be in DUMP format: https://www.veritas.com/content/support/en_US/doc/24427212-130506194-0/v99897177-130506194
For NetApp filers, Accelerator for NDMP supports only the DUMP format. Consult your NetApp documentation for specific details about its DUMP format.