I have been told that the front and rear xfer case output flanges have different bolt patterns
You need another front CV flange. Bolts right on, same spline size and count (front output and rear output). We suggest replacing the seal, grease it, and sand out the new flange where the seal runs on it and where the driveline attaches (surface it) before installing it.
My question is this: Is the part of the flange that actually centers the drive shaft the same for the front and rear?
Yes, the inner bore of the flanges are in a direct relation with centering from front to rear. I would use a 360° turntable and mill and center it in relation to the ID.
BigMike