As I understand it, inside-the-park-home runs are currently hard-coded as an extremely rare play with a frequency based on total home runs. While that's probably a decent approximation of current major league play, it breaks down in other eras and places. In the deadball era, especially in huge ballparks, ISTP homers were common.
46 of Ty Cobb's 117 career homers were inside-the-park. Jesse Burkett hit 55 ISTP homers, and only 22 over the fence.
To fix this in the game I think we need a ballpark factor entry for inside the park/out of the park homer percentage. For most modern parks this would be <1%, but for huge parks, or deadball era games it might be as high as 50%.
It might also help to have league totals or other behind-the-scenes numbers to vary the overall ISTP homer percentage by year or era.