How does one get both to hit the same point of aim?
Talking about short barrels and screw in chokes for turkey.

It's my understanding that it's how the barrels are soldered together and not user fixable. Doing it correctly is why traditionally a good SXS cost so much. Modern manufacturing has helped in this regard but it's still not perfect and a small percentage of inexpensive guns will have the problem.

If they don't already do so, then Briley can machine chokes that will bring make the adjustment. As long as the divergence is not to extreme.

You must have to send the gun in.
Can they regulate screw in tubes?

Double barrel S×S shotguns are generally "regulated" at the factory at 35 yards.
In my limited knowledge of the subject, I would think that if the tapping die lined up squarely with both barrels, squared up, well fitted tubes would (should?) not alter how the barrels are regulated.
He's retired now, but there used to be a gentleman in Decatur, TX that Purdey & Sons would allow to regulate one of their fine shotguns.

Yes, and you most likely will have new chokes.