What do you mean by “it”?
That you cannot claim the code or was this resolved by generation a new code as I suggested?
Please explain the issue in more detail as I don’t know what exactly is not working.
Did you start fresh?
Is the permissions problem with codec download for transcoding resolved now?
What did you do since your initial post and what is the exact current state of your Plex Server install.
I started a new docker instance. the claim code was not the problem, I just needed to give Plex a day to purge its old information and the claim worked without a hit, and no claim code required.
The issue I am facing is that when I am attaching the docker image plex to my account it is stating that it is Indirect. This in turn is what is causing the issues with the encoding, as the files are not getting to the stream fast enough thus it breaks. I am most likely going to just spin up a VM either in my ESX environment or in my TrueNas and make it as a stand alone entity instead of through the Docker App unless there are certain networking settings I could have set up wrong for this to work.
For information I have the following set up
1 NIC set up with a static IP address. No communication issues. (I am working towards setting up either a Link Aggregation or a Bridge of all my NIC once I have this system working with Plex)
Docker Image has had no settings changed from the basic install.
Doing that has lead to issues for me in the past. For me that resulted in remote access failing as well as libraries show up offline suddenly even though they were online.
If you use the old claim code for a new Plex Server install then it appears to have the potential to confuse the plex backend somehow as that still thinks that you are using the old server.
So if you destroy the local Plex Server instance and start clean, I strongly recommend to also use a fresh Plex Claim code in order to ensure that the plex backend knows that this is a new instance.
Can you provide a screenshot of this? I am not sure in which context it will show “indirect”.
The initial issue you reported was about permissions as the plex server could not store the codecs it had to download for transcoding - as I said I had the same when not choosing the “Apps” preset for the dataset. 
So i gave up on the app side and spun up a VM. All working within minutes.
The codec issue was not a permissions issue from what i see, it was am issue woth docker handing the transcoding off to the sharing side.
Of note, i do not have plex pass, so no claim code would ever come into play here.
I can only go by what you shared, based on that it did look like a permissions issue as you do get that exact error when the plex server is unable to write the downloaded codec files to the plex config folder.
so there might be a language barrier here, but when you replied the following, I did think that you used the claim token during the setup. 
Datasets also have an “exec” property which can override the +x.
Additionally, if plex is downloading codecs then it will need +w wherever its saving them
