With the release of pre-patch 9.0.1 for Shadowlands the upgrades of crafted draenor items are removed. You cant craft them anymore. E.G. Hexweave Cloth Rank 2-6. Same procedure on all other crafting Jobs.

It would be nice if you set it to unobtainable.

This should be fixed now as of (b8b8f05).

The base item remains craftable and obtainable, but the upgrade versions are now able to be marked unobtainable separately.

Also, 9.0 brought along brand new base versions of Inscription & Engineering WoD crafted items... so eventually will have to note how exactly to craft these new versions once it is figured out the specific requirements to do so.

You are correct. But unfortunately we do not currently have a way to set tiers 2-6 unobtainable without also setting tier 1 unobtainable, because they are all the same item id.

maybe you can make it configurable to display all tiers or display no item. Hardcore completionists can farm all transmogs and after finish, they can disable the ids from all tiers.

In my opinion there are already so many options in ATT settings that it makes it really confusing for users, so I'm not in favor of adding more options and more custom code just to handle those specific items. But someone else can certainly overrule me on that. Blizzard did say that they would add a way to obtain those appearances again in the future, so hopefully people will keep bugging them to do that, and it will no longer be an issue then.