Eric has it right IMO. My HT alignment fixture was made by Alex Meade. Here's a shot of one end of the HT fixture. Note the brass shim placed between the base and the tower. This is to tune the two towers' height, or to better make parallel the through rod WRT the table surface. Not shown is a mechanist's screw jack that supports the middle point of the seat tube. It is set to make the ST's center the same height off the table surface. Now the 3 points are established, the two ends of the HT and the center of the ST. A dial or indicator at either end of the ST will display any twist.
I first learned this as being the Bontrager method. Andy
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