I haven't paid attention to the flags for these in a hot minute so take my words with a grain of salt, but IIRC, the reason this issue happens is that it doesn't properly categorise the event as a break-up, but as a "secret third thing" that's still described as not being together in the flag description. I assume it was this way because they thought they might have to do content related to it in the future since it's a bit more specific, but then they... kind of didn't, leading to having to work with the more default paths. The "Illithid Alliance" flag is never used again in other files. It's only present in the Elfsong Tavern scene. It's the same for the "Stayed as friends" Spawn flag. Also never brought up in another file.
I'm not sure if it was force of habit at play there, since in the Epilogue they just add Ceremorph options for almost every dialogue line.
It seems likely to me this is what happened. I agree and would like to support the request to fix this for both of his endings.
