I had always figured the Hindmost Creche and the Great Mother to be the same thing (via metonymy as you say), and to be essentially the Hive Queen of the Pfhor. Their literal mother, laying the eggs that they hatch from, her dwelling thus being their nursery or creche. Of course a galaxy-spanning empire of organisms couldn't all hatch from one mother... which is why there isn't just one mother, and there isn't just one creche. There is a whole hierarchy of them, with the Great Mother at the top of that hierarchy, and her creche thus the hindmost in the sense you have described, as used in Niven's Puppeteers and in the real world.
I do however really like the idea of some kind of rampant AI or failed Jjaro (same thing in my book) being the queen of the Pfhor, and I actually considered at one point in writing Eternal having Hathor end up the origin of the Pfhor empire, her final vengeance on mankind (which is why the Sphere installation is still located deep in the heart of Pfhor territory). I'm not sure I agree on the idea that a Jjaro came down and took them under its wing though.
The impression I get about S'bhuth is not that he is a Jjaro who failed in some capacity and settled down to care for the S'pht, but rather that he is a S'pht who failed to become a Jjaro. This ties in closely with the theory that the Jjaro are AIs "evolved" from cybernetically enhanced organisms, and with S'pht "Royalty" being central controlling intelligences, in whose place have stood at times Pfhor controller cyborgs like we killed in M1, and rampant human AIs like Durandal. I think S'bhuth was a (even more) cybernetically enhanced S'pht which stood, as all royalty, in the same relation to a clan of S'pht as Durandal did once he took over for the Pfhor controller cyborg we killed. As such a cybernetically advanced creature, he was on the verge of being a Jjaro, basically went rampant, but failed to achieve that lofty ideal and just went nuts instead. ("Joined the chaos he had sought to evade").
I could buy the Jjaro having meddled with the Pfhor as well (why not, seems they meddled with everyone else), and the Hindmost or Great Mother being some kind of cybernetically uplifted Pfhor who likewise became superintelligent and went rampant and crazy.
But really I think, given the insectoid nature of the Pfhor otherwise demonstrated, that Mothers are literal biological hive queens and Creches are their palaces, and the Great Mother of the Hindmost Creche is the high queen of the entire Pfhor empire.
