Yeah a few thou I wouldn't be worried about. You have to remember that the disc isn't a magic "flatness" bullet. Your SFM is increasing by orders of magnitude higher as you approach the outer edge of the disc, so your grinding rates aren't remotely the same over a part. You can get relative flatness on things like scales with proper technique, but getting parallelism is extremely tricky.
If it's noticeably wobbling (I tried a couple of aluminum discs before switching to the neilson, which is what you appear to have, and it was much better than the aluminum ones), I'd check everything around the spindle of the motor, make sure it's clean and dirt free, and check the bore and keyway area of the hub. Deburr the keyway, and make sure you install a fresh key. Reusing the same one a dozen times will throw you way out sometimes because of the impressions from the set screw.
If it's not wobbling enough to make the system vibrate and make it difficult to ride the disc, then it's not enough to worry about. Remember, this is only a relatively precise tool. If you want real flatness and parallelism there are specialized tools that are huge and heavy for a reason (mill, surface grinder, etc.).
Why does the inside of your hub look so mangled up? Mine didn't look like that.
