Rattletrap,
You DO NOT have to separate the torque tube from the carrier. If your rebuilder is planning to do this then stop him and take it to someone that knows what they are doing. Separation is not required.
Yes, the heat of cleaning and bonding the powdercoating WILL destroy seals.
If your powdercoater is any good they will know exactly what to tape off (high temp) to avoid getting the coating on any machined surface or thread. If they don't do this then take it to someone that knows what they are doing. The only area you should have to point out to them is the area at the front where the u-joint ball has to slide on the tube. If you let them coat this area you will not get the ball housing to slide properly.
I can post pictures of the housings but can't until Monday or send me an email address and I'll send direct to you.
Paul Wisner