Huh, weird. I'd done Red on my first playthrough, did Spoiler for my 2nd, did Blue for my third, and Blond for my 4th. (Heh. I played this a ton some years ago because the FFXIV servers were absolutely fucked when Endwalker launched.) I can't rule out that Spoiler got priority for beating her for the first time, but you should get your primary conquest's ending as normal on further playthroughs.
I'd left off on a Black playthrough but I hadn't completed it because I was doing Hard Mode and Hard Mode just turned out to be kind of tedious rather than interesting. Some day I'll get back to this, it's a good actual game.