Okay, let's start
It's pretty straightforward that Naugus was responsible for the Silent Zone content, although without a certain time frame I believe the most that can be given about the feat is Tier 4.
In any case, full control of the zone is exclusive when it is within its territory, which makes it very "dependent" on it. Within the limits of the Zone where we could say that he is Low 2-C no other character was a threat to him. I think it's possible for us to leave Naugus as Tier 4 out of the Silence Zone, since it is said that he did it remotely, which I interpret to be outside of it, but inside the Silence Zone it would be Low 2-C or even 2-C (Since he fused the Silence Zone with the Void, both non-finite space-time pocket dimensions)
Yes, Knuckles has the power of a chaos emerald, but it's not something he really uses. The whole story of Knuckles being so powerful is what led to Chaos Knuckles. He has this power and he even manifested this "energy", but it was never something he controlled or used until he became Chaos Knuckles, where he actually demonstrated such power to its fullest.
This is indeed legitimate, but I believe that with Chaos having never demonstrated great feats with Chaos Emeralds could indicate that he does not use them "correctly". But this is my nitpicking
- Any other "that character used a Chaos Emerald" feat
I think by now we've come to something a little ridiculous. The big point of Chaos Emeralds is "they have infinite power, but you have to control their power". In the first Genesis Wave we saw Eggman affecting only one universe using a chaos emerald, but in the second Genesis Wave we saw him affecting all Sonic-verse universes (With the Megaman-verse) using a single chaos emerald as well.
The explanation for this is simple "It's the same source of power, but you need to know how to use it." Just a character having a chaos emerald and firing some burst of energy using that power doesn't mean that it's a low 2-C or higher energy blast.
But yes, Chaos Emeralds does have these Low 2-C to 2-A feats (Anyway, I have my problems with the whole "Great Harmony" thing). But except when Chaos used her (or when DeathEgg with Power Rings was able to match the power of one), they were always placed above most other characters as long as the user knew how to use their power.
- Tl;dr
- Naugus created the content in the Silence Zone outside her, so it's a justification for Tier 4, but the Low 2-C power is unique to him inside the zone. In fact, 2-C power since he fused two non-finite space-time pocket dimensions.
- Knuckles "with the power of a Chaos Emerald" most of the time it was just a power he never controlled, never used when he wanted to, and when in fact he awakened all that power and became Chaos Knuckles, he was above virtually everyone in the world.
- Chaos Emeralds actually has low 2-C to 2-A feats, but power is somewhat limited by the user's knowledge and how it can be used. Eggman could rewrite a reality using a Chaos Emeralds, or even infinite depending on his knowledge and resources (with Willy's help). Which makes their power totally varied depending on the situation.
But, they in fact survived a blast from Low 2-C characters and Omega did damage in Feist, with these feats not really having anything to say "they are false" (Unless we count "They aren't using their Low 2-C power" or "They got caught off guard"... or "Every moment later they are god-like against Sonic and the others")