I swear the brackets on the WRX and STI are identical. Are you saying they don't line up, or you bend them for more clearance? I can understand bending to give more room for the air conditioner line, but the only difference is the STI mounts to the outer hole on the passenger side bracket. There is a lot of play in the driver's side bracket with its two loose bolt holes. A good 1" left to right. If you have any trouble lining them up, don't tighten the driver's side bracket to the intake manifold. The passenger side bracket pretty much goes where it goes, almost no play, though. Tighten it down first.
A local and I test fitted and set the bracket side by side. Identical brackets, no problem getting the STI TMIC into the WRX with the WRX brackets. The guy I sold my TMIC to also confirmed the brackets I sent him (my facotry STI brackets, included just in case) are the same as his WRX brackets.
If there is a difference, I'd really like to see a side-by-side shot.