You are a little confused here, it seems. The automatic driveshaft or the STi 6speed driveshaft will work. Front axles will bolt right in to the transmissions. Rear axles are needed only if you go for the R180 (STi) rear diff. The rear axles are needed because the R180 is physically bigger and requires shorter axles. If you grab the ring and pinion off of a Legacy turbo, then you can convert your 3.545 rear diff into a 3.90 final drive that you need for the 6mt.
The drawbacks for retaining your rearend will be a weaker rear diff. The R180 is physically larger so it will hold more fluid, but it also contains a much better Suretrack limited slip. The drawback to putting in the R180, however, is that you need the STi axles. If you get the STi axles, then you need the R180 hubs. If you get the R180 hubs, then I believe you need the bigger brakes: commonly the Brembos. Cost increases almost $2k to install the R180.