As per CraigV - if there is a port conflict then it will cause issues , however as be does not directly use SSH or FTP there should not be (ubles sthis piece of sofwtare uses further ports (NDMP for instance)
Ther is another issue to consider - whether os not the transferred results can be snapshotted or are locked in some way. If they are lokced then you may not be able ot backup the results with BE afterwards (if that is your intention)
Finally I would not use the same volume for storage of the data transferred using this third party software as you use as a Backup to Disk or Deduplication Storage volume with BE itself as if you do you may run into complications/problems managing disk space
