Okay so here goes:
With an AP, you purchase a device that comes with pre-stored maps for different modifications done to a specific car. These maps are tuned generally for these modifications and not per each each. The unit will not recognize the exact car's response to the tune and change it accordingly. This device is also capable of storing custom maps that can be purchased from a tuner whether it be an e-tune, road tune, or dyno tune.
With OpenSource, one can purchase a Tactrix cable, a netbook, and download EcuFlash along with RomRaider to analyze and flash his or her car's map. This method is preferred due to the fact that the tune has what and AP's tune lacks, uniqueness. This method is used in conjunction with e-tunes for the most part. These tunes are customized for each and every car they are made for, however one must find an e-tuner to fulfill this task. There are many on both this site and nasioc that are very familiar with a Legacy GT.
I recommended that you do not get dyno tuned simply because you're stage 2. You're going to want to change something in the not-too-distant future and if I were you, I wouldn't want to shell out the price for an AP again for another tune.
I recommended getting a Stage 2 e-tune now since you can also change the parts on your car within 30 days of the tune for most tuners. You'll get the most out of a dyno tune, but is the extra 300-400 worth it (an e-tune is typically $125-175)?