First of all, I don't think this is a very accurate way to locate a part. When you tighten the part, there will be at least 1/4 rotation between tight and very tight. Using some sort of torque wrench might make that situation better, however I doubt you are going to get a very accurate alignment.
If you still want to do it, there are two ways..
If you were running production on this part, you would simply need to establish a constant setup. Common for all parts. (i.e. a hard stops to locate the part, automatic feed in from a set distance). Once you have it setup right, it should produce a constant result.
If this is a case of it being a one off part, I would cut the threads like normal. Then adjust it by grinding the contact surface between the 2 parts. This will of course alter the length of the part, but hopefully you have enough tolerance or the overall length doesn’t matter... If the length of the mated part does matter, I would make the thread 1st, see how the parts align at the required torque, and use that for a reference to fabricate the remainder of the part.
I have to admit I have never done this. I would personally not design something this way, because I don’t believe it would be accurate at all. But that doesn’t mean it hasn’t been done, and I could well be wrong about its accuracy.
Regards,
Ross Evans