The elytra is an amazing tool, but I found that personally I don't like how when not used it covers most of the player's back. So I thought, I'll use the morphic tool augment to make the bauble look like another body slot bauble. The infusion works and it did render the other bauble in it's place. However the elytra harness seems to be completely nonfunctional. I suspect this behavior might also apply to the Thaumostatic Harness.

That's a good point you've raised, but did you try the morphic armour system for it as well? If that doesn't/didn't work either, then morphic armour flight harness support is something that we may have to add in future.

It should be possible for me to add in support for the elytra, it's just a special case that I forgot when adding it. In the meantime, phantom ink or whatever it's called from botania also should work, if you have that. Also, is this an issue when using the thaumostatic harness, or is it just elytra?

I added Cosmetic Armor Reworked to my modpack a while back because it has cosmetic toggles for all Baubles. It adds toggles for armor as well but that duplicates Armourer's Workshop toggles too.

Phantom Ink does not seem to be able to hide the bauble. I will have to test the harness again sometime later.

Edit: The Thaumostatic Harness properly disappears with phantom ink. If you fly the sparks do appear, I guess that's not too bad. The Elytra Harness however does not disappear with phantom ink.
Also, using the morphic infusion (afaik you can't decide which, it's the same recipe) on either Harness breaks it's functionallity. They no longer have a vis charge either and they do not render.

Furthermore I tried making a caster gauntlet look like another. The result is that the gauntlet becomes the black and purple missing texture cube. I'm also unable to select foci, but I can toggle gauntlet specific things like tube connection.

Thanks for testing all that, the phantom ink problem can probably be looked into alongside giving the flight harnesses proper morphic armour support. And with the caster's gauntlet going strange when being used with a morphic tool, that sort of thing is likely to happen due to janky rendering and interaction systems being filtered through another janky rendering and interaction system, so I don't know if that can be solved or not.

The phantom ink was me forgetting to add the check in the renderer for that (I seem to be forgetting a lot of things lately...). I think I left the sparks in so that it didn't look like people were just fly hacking. As for the morphic stuff, a common thing you'll experience is that some things work 100% and others don't work at all. Unfortunately, this mostly depends on how the item creator decided to implement certain things. The most straightforward way to handle it is adding custom special morphic items to handle these cases (like I did for armor). So I would probably add a morphic bauble, morphic gauntlet, etc. As you can probably tell, this isn't very scalable, and while I probably want to get all Thaumcraft items working, I can't support every single mod ever. I might see about adding some sort of API that other mods can use if they like, though.