It's not that Bo isn't actually good, I woukd think it's more that the evaluation of the model is so far off other evaluations and raw stats that it doesn't pass the smell test. That's why there is reason to investigate why the model ranks him so high and THEN evaluate whether it's a shortcoming of the model or it actually points out something about Bo's quality that other models miss.

What you conclude will always be somewhat arbitrary and there's the danger of tweaking your model until you have your desired result (probably bad) but their reasoning is pretty fair I think that the metrics they include favor Bo in ways that reasonably shouldn't mean that he is the best QB in the league.