The deal was made because Kevin Cash, once scout for the Jays turned bullpen coach for the Indians, endorsed Gomes as a catcher to the Indians GM. Obviously someone in the org knew he was a catcher, it just wasn't someone AA valued, I guess.
Bautista, Edwin, and Donaldson are guys who developed with their bats late in their careers. Not the same as discarding a catcher by playing him at third and then seeing him be worth multiple wins the following season on defensive metrics alone. Gomes offense isn't even the biggest regret. It's the fact that the team so badly miscalculated his defensive value. Then you see how they handle their MLB team (with DH's playing LF, s***** framers like Navarro,, Bonehead at 2B, Reyes at short etc), and you realize that it took them way too long to see the value in defense (and it cost them $82m once they figured it out what Gomes was good at).
You are letting AA off easy by saying no one could have predicted it. Bautista breaking out offensively was unforeseen. A guy the Jays were paying knew Gomes was a catcher. Totally different scenario.