Nice meta-reasoning there for the Empire, Wes, solid, 10/10.
ICly, Yamatai does not know what threats exist beyond its borders, ICly, no one knows what exists on the fringes of the Kikyo Sector. It would be prudent for Yamatai to accept a military alliance which would consolidate the military might of the sector for the purpose of encouraging colonial expansion outward from the core clusters and further out into the fringes. ICly, the overconfidence and bravado which Yui is displaying is a disservice to her history.
More so, it was never about protecting Lor and Nepleslia, ever. Nepleslia and Lor can look after themselves if they so desired, by having their own treaty, with their own agendas. Instead, the treaty was carried out not to protect Lor and Nepleslia, but so Lor and Nepleslia could protect everyone else from Yamatai. Lor does not want another species to have to endure the hardship it has suffered through. Nepleslia has seen what Yamatai has been capable of since the beginning. Between Lor and Nepleslia, there is plenty of motivation to put a muzzle on Yamatai. However, even with that intent, there still exists the IC boon of cooperation between the nations, and the OOC boon of providing new RP opportunities which simply did not exist before.
If Yamatai rejects the treaty, and attempts to renegotiate, its very possible that the Empire could end up isolated from its neighbors, and treated as a pariah, due to the distinctive implications of Yui's desire to 'do her thing'. This display of indulgence in pride and wrath on Yui's part, especially in a forum such as the international relations conference, would only serve to polarize the situation, and likely set the smaller factions gathered against Yamatai in a steadfast manner, purely out of worry for what Yui may do when she 'does her thing'.
Frankly, from an OOC perspective, I enjoyed the treaty not for the muzzle on Yamatai, but for the fact that we could finally move on to something else other than the unspoken cold-war that had distinctively been a thing. From an IC perspective, the Matriarchy was happy to have a promise of new security for all parties involved, and to coordinate for that purpose.
What it comes down to is this: Wes, nobody is trying to sabotage, weaken, or harm Yamatai. We wish to protect it, from itself, because we do still love the heart of your sandbox, and we only want the best for all of us involved from an OOC perspective, and interestingly enough, that overlaps directly with IC interests.