good rule of thumb for every 12" back you can go up 1-2"
The water rises as it leaves the transom. When you go back 12 and up 1or 2 [ depending on the speed and a few other variables] the water actually hits the gearcase in the same place. If an increase of speed is realized it is from the balance and leverage change. Not so much from the more surfacing effect. To benefit from a more surfacing effect it needs to be raised more. That is provided you have the power and the boat is in a speed range for its size to benefit from a surfacing set up.
The handling will change for sure but the speed may or may not increase in every case. The boats that will benefit the most are the ones that run heavy in the water and respond little to trim. If the boat is already light and responsive to trim the change could be less desirable.
To Pauls point. Once a boat is molded its is what it is. How many manufactures actually go back and change the molds? Some of the high end boats improve their molds over time. Notches come in many different sizes. Plus a boat that is going to run at say 80 mph will likely enjoy a different set back then a boat running 100. Most boats are available with a range of engine options.
There are times when no matter what you do the boat runs the same speed. Different drives, ratio's heights ect make no difference. Maybe it does go faster but is twitchy and hard to control. Have you made an improvement or not. All depends on the individual. A race boat that is fast but, hard to control wins few races.
Ever wonder why the Fountains always have sand marks and touch up spots on their race bottoms? It is because even the slightest low spot has a huge effect on high speed boats. Point is the bottom is most often over looked when people are trying to make their boat go faster. Any short coming in the bottom integrity, surface or design has a huge effect on how fast it will go. In such cases changes to the set up may not change anything the speedometer does.
Say your designing a boat to race a particular class. The length limit is 30 feet. You know you want the bottom to be as long as it can be. You know the boat will appreciate a lot of set back but, you are working with a length limit. The extension box is not measured in boat length.
Possibilities and preferences are countless. My opinion is if the boat likes set back it is a better boat if it is built in to the hull. If the drives are in the basement too low re cut the transom and raise the engines.
It is hard to stay on point I will stop now.