Jeez, this took long enough.
Do you agree that Mogul's sixth sense is a power he only has in his master form as well, or only in its change of application?
The Chaos Emeralds
Throughout the series,
having multiple emeralds results in more power than one. We've only seen multiple emeralds fused together twice, each with different methods, whatever Feist's method was, we know he altered the emeralds by removing secondary effects. This is not proof that they are the same power, but rather proof that he can alter them.
All seven post harmony emeralds being required for a super transformation and the 14 pre harmony emerald strong Master Emerald being more powerful than all seven post harmony emeralds are blatant problems that only exist with the belief that the emeralds are thousands of times stronger and make it very evident that they aren't.
I acknowledged Ian's statement potentially presents issues, but I also mentioned that his explanation is a possible reflection of in-comic dialogue and that his answer, when removed from this explanation, is reflected in his writing.
The Sword of Acorns
The encyclopedia's take is…weird. It could be seen as a retcon of Sonic being shown as less proficient than Max, but I don't know why that would be necessary. It could mean that the sword can be utilized by basically anyone, which we kind of see when Sonic accidentally uses its healing ability, but the phrasing "master-level techniques" implies more than that.
Power Rings
It's not stated yes, but it's sort of half implied, it being a last resort, the ring's description and Nate utilization of rings for
different uses. This isn't an idea I claim as being definitive, only a possibility; it's also not the crux of my argument.
It seems unreasonable for a single power ring to be able to BFR to a different zone when warp rings can't do so without being charged with energy. It would also make much more sense for Nate to knock Naugus back through the already open portal than create a second one. Naugus getting knocked back by Nate is consistent with other high-tier characters being taken off guard, and the portal to the ZoS would close without him to keep it open.
The only thing that's required for the events we see to happen is Nate blast Naugus back with a power ring, enhanced or otherwise.
Power Null Resistance
Yes, Merlin thinks Sonic shouldn't have had access, but Finitevus doesn't question how he did, probably because he actively lets Sonic use it in 183.
Scourge being similar to Sonic shouldn't matter since this nullification is applied to the ring aura, lest Scourge present a plethora of problems.
Immortality
Accelerated healing isn't type 3 immortality. He'd have to heal from a mortal wound, which the ring aura technically did do in Mecha Madness, but not by itself. The aura retains his life force, to a degree, it kept him from being corrupted, but not from dying. Sonic Live is debatably not canon (Mobius Encyclopedia doesn't consider it canon, but I don't know if that's just a them thing) but past that, Sonic wasn't vaporized, it's explained an electrical storm caused the human's machine to
randomly teleport people through dimensions, this is why Sonic ended up in the in-between zone. There also is no statement saying Sonic was vaporized, like I said in the OP, that's a quote from the Sonic News Network.
Light and Dark Mobius are possible futures yes, but they are also separate zones. The Sonic of Silver's past is not an alternate Sonic, it's the prime Sonic, Silver is from the prime Mobius, his past is Sonic's future. If Sonic didn't die in Silver's past, his story doesn't happen. If you want to get super technical, the actual story we read in the comics is an "alternate" timeline, because Silver went back in time and changed things. The only "unaltered" timeline is the one without Silver, where Sonic dies, leading to Silver's present.
The Mephiles death should not be ignored, because it happened. We're told 06 happened and including it doesn't create any problems. I haven't played Chronicles so I can't say for sure, but the encyclopedia's page for the Nocturnus Clan makes it out as if the plot of Chronicles hasn't happened yet, with them not yet escaping the Twilight Cage.
Post-SGW Chaos
I understand Chaos can control the world's oceans due to being a water god, but just like benders in Avatar, controlling water doesn't necessarily mean you're physically that strong. The fight with the Dark Guardian took place underwater so Chaos could utilize the ocean to fight, he needs to show he can utilize that strength himself. (unless he has, but again I didn't look into this one)