First, Judas as a Hero does count for Boat. As long as you convert him and put him in Boat, he counts for it.
Second, I'm not so sure I agree with browarod. You can, for example, band to and then exchange your opponent's AutO with a Judge in your deck. Exchange basically means that two cards have to change places, but that isn't actually happening because AutO still goes to your opponent's deck per game rule.
I get where the concept of the ruling comes from for the cost-benefit, but I believe that there is enough precedent to say that it ending up in the proper deck per game rule still satisfies other wording, and I can see that applying here, too.