I don't see anything weird about Conrad having blond hair. He could've easily got that from his mother and if I'm not mistaken, that's what was said in the game at some point. Think Sera pointed that out to the King when he became paranoid at the dinner. Before naming Elis heir. Either that, or someone in his recent family had blond hair.
Not to mention, I don't think the dev is going to do anymore of these bloodline twists. It's already getting complicated to keep up with as is. If they keep adding more on top of it, it's just going to turn into an incoherent mess.
Since it's currently unclear whether the Red Emperor's hair was black or brown, Conrad's lineage cannot be definitively confirmed. Theoretically, if the Red Emperor had dark hair, his descendants would at most have brown hair, and it's unlikely that any would remain blond into adulthood, even if their mother was blond.
I've seen one parent with brown hair and one with blond hair, and children with blond hair from infancy that gradually darkened. But I've never seen a child with blond hair under these circumstances.
Perhaps I'm not well-informed enough, or perhaps I've been misled by George R.R. Martin. I'm still confused about the Red Emperor's true cause of death. What happened to Regis's imprisoned brother? And the fact that Regis was killed while Elis was peeking into the past doesn't seem realistic. Is there some secret behind this?