Part of me likes the idea. It explains that line from Makes-Things, which previously didn't fit with the currently canon history. It also adds some back-up to the never-quite-spoken-aloud idea that There's Something About World One that makes it a particularly time-rupturey and delicate version of Earth, closely linked to the rest of the worlds.*
But on the other hand . . . I guess it just feels a little too forced? Above you asked, "How did the PPC go from slow enough recruitment that the first three agents worked together for a significant amount of time before there were six agents total, to masses of agents during the Insanity Epidemic, in the space of maybe 5 years?" Let's go by Occam's Razor, based on what we already know. The first two weren't recruited; they fell through by accident, due to Makes-Things. We know Osbert was the third; maybe Osbert was the first to fall through a natural plothole (EKYL PLESE GIVE OSBERT A BACKSTORY), and at least some of the other seventeen probably came the same way. We already know the SO wanted to move away from "blow up the planet" to "deal with just the bad parts." Seeing how effective the World One recruits were, and perhaps starting to get an inkling of World One's status as a story nexus of some sort, perhaps the Flowers started their campaign of recruitment posters and the like then. Such posters are mostly mentioned in older spin-offs, indicating that that recruitment strategy was used more heavily in the early days of the (real world actively written) PPC, but have tapered off more recently. This could be an indicator that the upsurge of staff you mentioned between the early days and the Somebody's arrival was due to this stronger recruitment campaign. (Radio Kunek's history seems to be a poetic telling of events similar to what I've just described. At least, that's my interpretation.)
As for the line from Makes-Things: Maybe with all the humanoid recruits the PPC started to get, they put another level of supervisor under the Flowers to deal directly with the other (mostly) human(oid) agents. But perhaps that didn't work out well, or perhaps they simply preferred having the non-Flower supervisors in the field, or perhaps said supervisors were spending to much time in the field to do their jobs effectively? Any of which could have led to the Flowers reinstated the original department heads as the direct overseers to the agents. Doctor Fitzgerald's continued role as department head may simply be due to his better understanding of humanoid biology than any of the Flowers could manage, making it more efficient to keep him on as head of Medical. (Plus, our version is a hologram, right? I've never been quite clear on that.) If this happened not long before Jay and Acacia's posted mission reports (or even during the first four!), it might still have been on Makes-Things's mind when he introduced Agent Dann to the Marquis.
So, yeah. I guess, in general, I prefer using what's already established as a base for writing around, rather than adding big changes like this into the PPC's backstory. And I feel like we do have enough holes to fill, as is. Putting aside Ekyl's personal investment in Osbert, there are at least two or three long histories that could be made out of everything I've just discussed. I vote against this change.
Also, completely off-topic, but this is a photo from New Caledonia:
*I'm fighting it, because I know I shouldn't think it, but I'm getting more and more convinced that the PPC's "World One" is Stephen King's "Keystone Earth" from the final Dark Tower. They both have exits and entrances to other worlds, they both have a strong theme for the power of stories, and while Keystone Earth is the Earth closest to the Dark Tower, which is the center of all worlds, World One seems to be closest to PPC HQ (based on the disproportionate amount of recruitment from there), a location situated between other worlds. There's also the whole "coincidence is dead" thing, which ties nicely into two separate PPCs. I'm sure someone will publish a Dark Tower mission that contradicts this someday, but for now . . .