I suspect this may be a way to discourage players from leaping into places that could cause injuries. Also, there is the potential for a "lack of consistency" in the results of a play in two respects: 1) depending on whether a player chasing a ball into the stands is from the home team or visitor's team; and 2) depending on whether a player chases a ball into his own team's dugout or the opposing team's dugout.
You're probably right. Owners invest millions of dollars in these players now, and while we're thrilled when somebody makes one of those plays, they have to cringe as they watch one of their commodities risk a faceplant on the dugout steps.