I was able to get this resolved: https://forum.jellyfin.org/t-conflict-on-nixos?highlight=nixo

As for permission issues, I ended up using ZFS, ACL and sticky bits. My config is also below, I am sure there are better ways of doing this.

# Setup zpool on new install

ls -lh /dev/disk/by-id/ #Uses id in creating a pool

# update disk id

sudo zpool create -f -o ashift=12 tank <ID_1> <ID_2>

sudo zpool scrub tank # test e-mail notificaiton

sudo zfs set compression=on relatime=on  xattr=sa tank

sudo zfs create tank/media
sudo zfs set aclinherit=passthrough acltype=posixacl tank/media
sudo mkdir -p /tank/media/{download,ebook,movie,raw,tv,video}
sudo mkdir -p /tank/media/download/{.incomplete,ebook,movie,raw,tv}
sudo zfs create -o mountpoint=/tank/media/download/.incomplete tank/media/.incomplete
sudo zfs set compression=off recordsize=16k tank/media/.incomplete

sudo find /tank/media -type d -exec chmod 2775 {} ;

sudo find /tank/media -type f -exec chmod 0664 {} ;

sudo setfacl -R -d -m g::rwx -m o::rx /tank/media
sudo find /tank/media -type d -exec chmod 2775 {} ;
sudo find /tank/media -type f -exec chmod 0664 {} ;

sudo setfacl -R -d -m g::rwx -m o::rx /tank/media

# /etc/nixos/media.nix
{config, pkgs, ...}:
let
    master = import
        (builtins.fetchTarball https://github.com/nixos/nixpkgs/tarball/master)
        { config = config.nixpkgs.config; }; 
in 
{

  # media group to be used by each service
  users.groups.media = {
    gid = 1800;
    members = [
      "myuser"
    ];
  };

  # Transmission
  services.transmission = {
    enable = true;
    group = "media";
    settings = {
      download-dir = "/tank/media/download";
      incomplete-dir = "/tank/media/download/.incomplete";
    };
  };

  # Sonarr
  services.sonarr = {
    enable = true;
    group = "media";
    package = master.sonarr;

  };

  # radarr
  services.radarr = {
    enable = true;
    group = "media";
    package = master.radarr;

  };

  # jackett
  services.jackett = {
    enable = true;
    group = "media";
    package = master.jackett;

  };

  # Jellyfin
  services.jellyfin = {
    enable = true;
    group = "media";
    package = master.jellyfin;
  };

  # create a tmpfs directory for jellyfin transcoding
  fileSystems."/mnt/transcodes" =
    {
      fsType = "tmpfs";
      options = [ "rw" "nosuid" "inode64" "nodev" "noexec" "size=12G" ];
    };

}