Layers
Starting with the layers, Hard no for the Durability Negation layers. I don't even think Gwen should have that resistance given the sonic blast used on her in the scan match the one mentioned in the description, however I'll ignore that and assume it's resistance. That still doesn't mean they get layered durability negation since the other feats you mentioned are of a completely different attack. Gwen surviving a sonic blast that can incapacitate people through "sound" is not the same as bypassing someone's durability through absorbing powers.
The Transmutation layer might be the only one I agree with and it's mainly for the turning Ben into liquid and the last one that doesn't involve the green flash. Since the rest is crossed out, I'll not discuss it. I'll comment on the power additions next.
Abilities and Resistances
* Omnitrix
Where is the scan of Rex failing to control the Omnitrix? The first scan just links to the Generator Rex wiki that says he can control technology, and the next scan links to a statement about the Annihilarrgh being able to destroy the universe... Edit: Nevermind, I see the scan all the way down on Kevin's intelligence update. The resistance is fine.
As for regeneration, where does it mention his entire physical form was destroyed? That just shows Ben vaporized and then him fall down with smoke on him. He could have been reduced to molecules or atoms for all we know, and since we don't immediately use the highest interpretations, it would likely be High regeneration unless you have a statement that supports Low-Godly.
* Alien X
It would be Power Nullification, not Resistance Negation.
Existence Erasure on those levels seems fine.
* Chrono Navigator
Existence Erasure on those levels seems fine.
* Annihilarrgh
Existence Erasure on those levels seems fine.
Note: What's on Toppo's profile is irrelevant, this is Ben 10, not Dragon Ball.
* Gwen
Matter Manipulation on a molecular level is fine.
* Mana Manipulation
All the additions seem fine.
* Anodite Physiology
I'm neutral on those resistances. Mana has multiple uses but they all don't passively have that effect at once, the scans for mana show it can be used for different things, you'd need to show they can resist those specific abilities from Mana.
For example, Gwen used her mana in that one scan to specifically effect that portal on a molecular level, however, this doesn't mean a standard mana blast from her natural hits at that level.
I think the Aura additions are fine, though the last scan "cloud kill" one doesn't work for me.
Intelligence
* Kevin
While I think Kevin can pass for the later stuff, that scan is not justification for "Great knowledge on astrophysics", he's just using that as a metaphor for the birds and the bees because of what Celestialsapiens are. Nothing there shows knowledge on astrophysics, let alone great knowledge. Same goes for the scan of him saying he can hack the Omnitrix, not only did he goof a bit at the beginning, he's making an assumption of his past interactions with it which isn't enough to suggest he can pull it off.
However, him making a machine that can reboot tech like the Ultimatrix (something real life genius wouldn't be able to make) and having knowledge on multi-dimensional aspects of mana back with his Plumber knowledge of the various interstellar laws, technology usage and so on, I could see Extraordinary Genius.
* Gwen
Genius is fine.
Those are my thoughts.