This sonds like configuration issue in the dataset. What you need to do is make sure the qtrees are in the dataset not the volume, this means non-qtree qtree "-". My guess is that in the dataset you have the volume itself and the qtree and that PM is only vaulting the qtree not non-qtree. What you should have is the "-" which represents non qtree data and the qtree.
Snap Creator will read the dataset members, you should see this in the output. Snap Creator should read the non-qtree-data and the the qtree and then register the snapshot with those members. Can you also send output of the logfile, this would show if dataset members are registered correctly?
For a workround solution you can have SC do the snapvault if you want to. Just turn on NTAP_SNAPVAULT_UPDATE=Y and set SNAPVAULT_VOLUMES to whatever you have in VOLUMES.
Re: SnapCreator and Protection Manager using default pm backup policy behavior
Yes is is a requirement that SC create dataset either through GUI or CLI. The dataset which SC creates is an application dataset. PM will not acknowledge SC snapshots unless the dataset is application dataset.
SC will create a blank dataset so you should be able to re-build it quickly.
Here is a video on how to do this in GUI using existing relationships: