Justin,
Certainly if the par 3 is reachable to the long hitter and not the short hitter, that favors the long hitter, just like a par 5. So, I was thinking more of reachable for both, but less than a driver for long hitter.
I think the distance control is the hardest part, by far, so you definitely have a good point there. But, in my mind a good par 3 of this length will not be too exacting/punishing, so there should be room for imperfection. The hole may come down to my having to get up and down from 50 feet and the bomber 40, but if I'm giving up a lot of length, hopefully that plays to my advantage. Especially now, the gap between driver and 3 wood can be quite large, more so for bombers, so that can be an issue. I'd like my chances taking something off a driver compared to someone trying to lean on a 3 wood, for example. And at this distance, all players distance gaps should be fairly big, so everybody's adjusting to various degrees. And if a dinker is to be competitive at a high level he's probably got relatively good distance control even on the driver as he's not hitting it that hard, etc.
At the end of the day, I feel that any hole that makes scoring more of a contest of course management, a long two putt, getting up and down, etc. should help the shorter man as he should be better at this (given that the players are of the same total skill level). But if only one can reach or the shot requires a towering soft shot the short man can't produce, this is all out, and it's obviously in favor of the bomber. (Here I agree very much with Ken's assessment of the situation.)
This is how I feel with regard to my game, but I typically think it's generally applicable. I think you're right that it's different for the truly elite, if you can hit a high 270 2 iron on a dime, you're in much better shape than anybody else hitting driver or any wood. I'd love to see some statistical analysis on this, but I don't know how that'd be possible with existing data.