Yahiko didn't see a perfect jinchuuriki—at this time potentially the only person able to control a bijuu not named Hashirama or Madara—be a zombie to this mysterious sharingan wielding man in the shadows.
I mean, what's more believable? A random kid from Konoha stumbled onto mysterious powers and can take over your home village and your leader?
Or the almighty, legendary Uchiha Madara somehow survived and has been running things in the shadows?