@kickhiminthenards Okay, I'm kinda shooting from the hip here, so please bear with me.
It sounds like a mapping & permissions issue. My fellow mod @Theo posted a really great tutorial on how to install RADARR which I just followed this past weekend. In it, he shows how certain directories need to be created and "mapped" for the app - in this case radarr - along with setting certain permissions. Because Handbrake will be similarly run as a container I suspect there are parallels here.
THIS video shows how to install Handbrake in docker (container) and maybe there are some clues as to how to properly configure Handbrake installation via TrueNAS.
I hope this is even a little helpful and if I'm off-base here, my apologies - totally not trying to send you down the wrong path, only help figure out how to pull this off.
If you DO make some progress, please keep this thread updated as I'm certain others would LOVE your feedback.
Best of luck!!