i actually just put an STI top mount on my wagon about two hours ago. The topmount was off an 04 sti, and my wag is 07, so they are both fly-by-wire. However, my advise is get a silicone Y pipe. the fit will not be 'perfect' but a silicone Y pipe will give you enough flex and play to line everything up.
...I didnt get one, and it was a PITA lining everything up. I had to cock (no gay) the intercooler and clamp the piss out of the turbo outlet elbow, then tilt the intercooler back to line up the mounting bolts...happy with the end result though. good luck.