This is a pretty standard practice. The rig is built aligned to the axis, so that calculations and information has a clean base to start from. So the rig is made in the T pose, but the character is skinned and point weighted in the relaxed, 45 deg. pose since that's better for modelers to work with and yields more natural results.
What you need, is some kind of pose library. Check in the script section here for poseman or something similar.
Then, what you'll do, is build the rig in the T pose, and save that pose to the library. Then position it in the relaxed, 45 deg. pose for skinning, and save that pose as well.
Then, if you have to rebuild the rig, go to the T pose, rebuild, go to the bind/relaxed/45 deg. pose, and skin the character to it. That's the general idea... I can't go into specifics since I dont' know how your actual script funtions. Hope this helps.