Si drive can control boost because the S modes are mapped to something called "requested torque" and this is used to determine throttle plate opening %, wastegate duty cycle and target boost. Each S mode can ask for different boost and set a different wastegate duty cycle in order to hit it.
If you combine this with some other tables that control requested torque per gear, you can very effectively control boost with nothing more than a 3 port EBCS and proper tuning.
For the stock turbo 08+ STi E85 tunes I do, I generally setup S# to hit 23 psi in every gear and hold as much boost as possible to redline. I setup S mode to hit around 18 in 4th and a little less in lower gears. This amount is pretty nice for the street where 23 psi can be too much and you don't have to remember to disable TC so it doesn't come on. I tune I mode for economy and it only hits around 13 psi. Most people seem to really like this setup.
I've never really understood the benefit of a hybrid boost control setup. I feel like a good EBCS and a good tune work much better than anything else but I'll admit that I haven't spent a whole lot of time looking into it and I've never tried it myself.