When you specify the transcode dir in the PMS Linux server it only changes it for media actively being watched. It does not change it for shows being transcoded so they can be plex pass synced to a device for offline viewing...
I have limited space on my root file system's drive and had to resort to a symbolic link hack so that the sync data will be transcoded to a nas share.
It seems to me like this option is a no brainer since we already have the ability to move the transcode dir for actively watched stuff and if we're syncing a lot of content it can take up quite a bit of space on the PMS's local disk.
I came across this as well and was surprised to discover that the transcode directory setting is not applicable for the sync transcodes.
Running on Windows with the OS and PMS residing on my small SSD. There just isn’t enough space to keep lots of transcoded sync content. So in the end I created a junction to work around this but I’d rather see this as an option.