Last questions first: the Protectors of the Plot Discontinuum.
First questions second: the diagrammed version of fanfic-Word World relations is a bit simplified. I've added an explanation section and diagram to the doc, with the writing running as follows:
This is in actuality somewhat oversimplified. The effect is not limited to some vague ‘destabilising’; it’s more akin to fanfic creating a puppet with a loose connection to the original. While one such puppet being jerked around won’t change the canon much, many of them being pulled in the same direction will drag the canon around after them.
And, curiously, this effect is not limited to the Word Worlds. The Department of RPF have long known that ‘real’ world people can be affected by badfic; indeed, every ‘girl falls into Canon X’ story can be deemed to affect the author who bases the ‘girl’ on herself - this explains the strong emotional reactions they often have to their character being maligned. In fact, there is a strong argument to be made for Word Worlds simply being parasites writ large - think of the alterations to New Zealand following the release of the Lord of the Rings films. One could claim them to be simply a sensible business decision to attract tourists - but one could also claim that the increased mischievousness of twins across the multiverse is simply whimsy. That there is a ‘reasonable’ explanation does not exclude the base cause being fanfiction.
The only alternate explanation which really fits the evidence is the Suedom model, wherein the canon simply loops endlessly, and different badfics happen on different iterations. I'm avoiding that because a) #Idon'tlikeit, b) it seems fairly brutal on the canons, and c) it requires a lot of pinpoint time travel. ;)
As to the idea of all the worlds being equally extant... well, part of that (RPF) has been mentioned in the above expansion, and actually expanded a little. But your main thesis... doesn't work in the context of the PPC. J.R.R. Tolkien can power HQ by spinning in his grave because it's his creation that's being mauled. And, well, in all the PPC missions, we've not only never seen, but never seen mentioned, a mission into a story written anywhere other than World One. It just... hasn't happened. Which, to a physicist, strongly suggests it can't happen.
Then there's the fact that a qualitative difference between Word and Atomic worlds is a firm part of Origins, to the point where Reality Rooms work because Mary-Sues - from Word Worlds - can't survive in Atomic worlds, because their plotholes stop operating.
So no: in the PPC universe, the creative process is definitely one-way. New creations can change the canon - this is clear from the way Legolas is now blond, and was shown in HFA when a new book came out (I forget which): new characters appeared in the canon. (Though of course HFA is a fanfic itself, gold rather than red)
And on a personal note: your theory removes all creative power from authors. As someone who likes to think of himself as rather creative, I find that to be a fairly big flaw in the argument. ;)
That said, the distinction between Atomic and Word Worlds isn't as ironcast as the writer makes it sound. The example of RPF, and Word World parasitism, shows they are of fundamentally the same kind - and plotholes from the Cascade, which ought to only appear in Word Worlds, showed up around Origin...
... all right, I'll spill. From an out-of-universe perspective, written worlds fall into (at least) three categories:
Cat. 3: Fanfic. These are the stories where Agents can read the Words. They're total parasites, with no stable existence - once the author insert (of whatever kind) is killed, the dimension dies.
Cat. 2: Word World. The original canon. Here Agents probably can't read the Words (I don't recall seeing it, anyway), but Flowers still detect them. While still somewhat parasitic, they're pretty stable; a PPC agent couldn't do something to kill a canon dimension.
Cat. 1: World One. The 'real world' of the PPC Multiverse. Neither Flowers nor agents can detect that it's made of words - but, er, it is, because we're the ones writing them. ;) Origin falls into this category - I mean, come on, it has natural plotholes. Even if you can't actually sense Words, that's a big hint that they're there.
Cat. 0: The Real World. Our world - our actual world, not the fictionalised one where there's a PPC city in New Cal. As far as we know, this isn't a Word World at all. (;^-^) Nor has any PPC character ever set foot in it - because there's no such thing as portals from fiction into Actual Reality. Again, that we know of... and if there was, you couldn't read about anything that happens on this side of it, because this side has no Words, and no narrator...
hS will stop here because words