First, that three-layer idea from the last post was an approximation, based on the information that I've gathered from both the Board and the missions. I am fully aware that it's got its rough spots and bits that don't fit in, but it's what I managed to assemble so far. If the model doesn't work, it doesn't work, and it can be scrapped and somebody can come up with something else.

Do you have ideas for a modification to the existing idea, or a better idea for rationalizing the SEP Field with the canon-protection effect? Input from other people would help fix up some of the shaky spots.

There are also a few holes in your "technology=boring stories" reasoning: it's not about whether or not what happens in the mission is caused by the canon shielding the agents or an augmented device shielding them or whether the agents just took the opportunity to jump behind a bush when a Sue looks behind her, it's about the story, and whether it's well-written and worth reading.

There's a difference between "PPC technology doesn't develop much because Finance isn't made of money, it only works with it, and DoSAT is more about fixing things these days anyway" and "PPC technology does not address one of its fundamental problems". Agents shout, and babble, and throw things, and all of that. This is not wrong, and is in fact fully expected, since the Sues and other canonical distortions are busting up the worlds we know and love, after all, but it poses a potentially dangerous problem, since, as we see in TOS and several spin-offs afterward, the canon does not make it so that the Sues cannot hear you, and if you make enough of a scene, even the canons will notice you.

Thus, a large percentage of Sues would find the Agents assigned to her when one of them starts breaking into a rant, or going bonkers, and then could break the storyline and attack them, or be prepared for being attacked, and cause untoward danger to the Agents. The PPC is terminally understaffed, and if a personal quirk of the humanoid agents results in lots of extra work for Medical, with the possibility of the PPC then becoming even more understaffed, the only options become either forcing that trait out of the Agents, which is inhumane even by the Flowers' standards, or upgrading the technology to let them rant in peace without the risk of suddenly being ambushed by Boromir's non-canon niece who can blast rapid-fire lightning bolts from her hands.

You can make a mission funny and well-made without having the Sue spot the Agents, or having that be a significant risk. It just has to be handled well. A good story is always in the execution.
Even with an SEP Field up, it could fail spectacularly, as the CADs often do, or certain in-fic circumstances could make it less than useful, if you really want to go the "we have only our disguises now, and nothing else" path, or if you want, you could ignore the presence of the SEP Field outright or cause the Agents to have disabled it in their flash patches for whatever reason. But there are plenty of ways to mess with the agents using what the badfic already creates simply by way of being badfic.

You're right, having the Agents sit in their RC reading the badfic while a little camera-robot or something goes to kill a Sue would be no fun. That is why we do not write it. This world is, when you get down to it, a series of stories about making fun of other stories, and therefore, a large portion of them must be fun to read.
If something is implausible, the writers in the community can address that, and solve it in-universe, and if something isn't fun, then that can also be addressed. If someone tries to make something easier, it can become less fun, but if someone does something the "hard way" and doing so becomes implausible, we should fix that as well.
And, yes, I am fully aware that "implausible" has a different meaning in a world where an organization of trans-dimensional fiction police travel through literal plot holes on the orders of talking plants. But something can be strange without being problematic.

The PPC using enhanced technology isn't going to ruin the way the stories work, because unless it's something everyone likes, not everyone is going to accept it, and that's okay. On the flip side, we have a formula for how our missions normally go, but that doesn't mean that everyone has to stick to it exactly, or else every new story would read like every other older story, and the plotlines and characters would become boring and cookie-cutter.
If there's inconsistency, it should be ironed out, but nobody should be forcing their ideas on anyone, and that's not what I'm trying to do here. There was a problem. I'm doing my best to find out how to make it less of a problem. My idea might not work. It might need substantial revision. But that's okay, because there are far more people who would have a stake in this than just a select few.

Okay, this went on for a lot longer than I thought it would, but I hope the points I was trying to make didn't get lost.

Oh, and a postscript on the D.O.R.K.S. I don't think I've ever seen the D.O.R.K.S. being absolutely useless. Difficult to use, yes, irritating, yes, occasionally hard to find because it turned into something very small, yes, but never the device just not doing what it was intended to do. If a D.O.R.K.S. didn't work, people would stop writing about them, because there's really only one joke in the "I tried to change my disguises, but it turned out that my D.O.R.K.S. won't work." premise, and it's right there in the premise.

Since technically she's a canon character, to some extent, Layer 1 wouldn't work at all, and she would be more susceptible to effects from the Words that claim that "all the elves" or "every elf in the room" does something, but I'd think that her distance from her home continuum in recent years has lessened some of the restrictions this may have had on the SEP Field.
It wouldn't have removed them completely, obviously, since some part of her would always be whispering "What are you doing over here, hiding under that bush dressed as an orc? You should be in your true elven form, standing behind Legolas where you belong!", and the Sues and Stus would probably be able to pick up on that, since the canon characters not perfectly falling into line would prove a problem for them, and thus would make them able to see through her SEP Field.

I just realized I spent a paragraph saying what you already said in one sentence, but in longer and more specific terms. +2 Rationalization Points!