Figured out this was nothing to do with what I was doing in docker or fileflows mapping. I use a program to auto mount shares on my Mac to the volumes location due to inconsistent mounts using the native method. Turns out even though the share I needed access to was mounted to volumes it was set to be hidden in network locations on my NAS. Once that was fixed it was visible in both locations and now the node runs as it should aside from hardware encoding.
I made a dummy flow to check which hardware encoders were available on the node and the Mac always defaults to software encoding. The flow works because it outputs intel quicksync for the NAS.
There may be something I need to find now that the node is running in docker desktop.