I also think it's an odd situation. The OP said that the valve was within a penny's width of where it should sit, so I think we are talking about the last thread that the valve contacts. If the tap only cleans up that last thread, I don't think this is a big issue, especially this the bottom threads tend to be incomplete anyway.I find this a little wierd. Tapping the neck is part of the manufacturing process, since it involves metal removal and could (if badly done) effect the strength of the neck and threads, which are critical to the safety of the tank. And the tank is supposed to, as I understand it, be hydroed after the manufacturing process is complete, to insure that everything went as planned. Come to think of it, how did they ever hydro it if the threads were incorrectly formed?
So you or the shop shouldn't be finishing up the job of manufacturing the tank. If the tank wasn't made righ, then they ought to give you a new one, or at least get it back to the factory so they can be sure the job is done right. Sending a tap so you or the shop can finis the job is a bit like sending you a hammer if the tank was dented. Sure it'll probably turn out just fine, but it isn't how it is supposed to be done.
I may be overreacting, and would be interested in hearing Mike's comments on this.
Then again, if it were my tank and I had no other choice, I would eat the shipping charges just for the piece of mind.