You are correct to reason that the bookmaker has probably not applied the overround equally to all runners.

  It's more likely that a runner's share of the overround is related to the amount of money they expect to take on that runner and given the favourite-longshot bias, your suggestion of short price favourites having a larger share of the overround seems sensible.

If you have a sufficient amount of data on bookmaker prices and race winners, and assume a specific relationship between a runner's odds and its share of the overround then you can find the parameters of that relationship which maximize the likelihood - in other words, the adjustment to the raw bookmaker probabilities that result in the most accurate predictions of the winners.

You are correct to reason that the bookmaker has probably not applied the overround equally to all runners. It's more likely to be a function of that runner's contribution to the book and the amount of money they expect to take on it.

If you have a sufficient amount of data on bookmaker prices and race winners, and assume a specific relationship between a runner's odds and its share of the overround then you can find the parameters of that relationship which maximize the likelihood - in other words, the adjustment to the raw bookmaker probabilities that result in the most accurate predictions of the winners.