The coin was hand struck in 1609, a time when the alignment of obverse/reverse design was not routinely performed with any accuracy. Even with the introduction of milled coinage and screw presses, the alignment could vary as each die wore out and was replaced. Precise and consistent alignment would not appear until hubbed dies and steam powered presses were introduced in the very late 18th century
There are several levels of effort that go into slabbing a coin. Unfortunately, the level that is involved in typing the text that goes onto the label is not the same as the level that assigns the grade.
Be wary of anyone trying to sell you a coin from any shipwreck without a legitimate COA. As mentioned, Atocha and some others carry a "perceived" premium so you can see the incentive to claim its from a particular shipwreck. Also, silver replicas for jewelry were made so just testing for silver is not sufficient to authenticate that the cob may be genuine.
You can collect 8 reales cobs that are not damaged by exposure to seawater. These are, of course, easier to assess for possible authenticity since the weight would not be diminished by corrosion and the coin design should be better defined. With shipwreck dreck you have only the reputation of the issuer of the COA to trust.
Consider this -- how would someone else be able to authenticate this coin if you lost the COA?
The NGC census shows 7 straight-graded in equal or better grade. Can you find any auction results for the straight-graded ones? HA has only sold 3 "details" graded ones.
There is no standard to apply to "details" grades. The XF is clearly superior and may be very attractive to collectors (very likely outside of the USA) that don't care about TPG grading.
The correct approach is find examples of regal issues and then study the differences between them and your example. The big auction sites have many examples of these for you to view.
Hard to say if it is a genuine die as these were never released from the mints without significant defacing to prevent counterfeiting. The few photos of dies that I've seen have all been round. There were no hubs at this time -- all dies were unique having each element struck from individual punches.
The market for such items is really small so it's really hard to place a value on it. You should show it to experts to determine if it might be genuine. However, a contemporary counterfeit die would still have value to certain collectors.