Understanding beta binomial regression (using baseball statistics)

In this series we've been using the empirical Bayes method to estimate batting averages of baseball players. Empirical Bayes is useful here because when we don't have a lot of information about a batter, they're "shrunken" towards the average across all players, as a natural consequence of the beta prior. When players are better, they are given more chances to bat! (Hat tip to Hadley Wickham to pointing this complication out to me). That means there's a relationship between the number of at-bats (AB) and the true batting average. For reasons I explain below, this makes our estimates systematically inaccurate.