You are doing it the best way. All barrels are curved to some extent. Ignore the other end. When on the chamber end you want to notate the high spot so you can clock it at 12:00 on the action. I dial the throat and then 2" farther in. Then thread, bore and chamber with the 2" portion dialed into perfection. This get's the bullet a straight into the bore as humanly possible. Do the same on the crown and muzzle threads to get the bullet out of the bore as straight as possible.
And where did you get this info? Off the internet probably. You couldn't make a bore banana shaped if you tried. They may not be perfectly straight, but they ain't banana shaped.
Give me a list of the winning competition gunsmiths using the Gordy method.
Now tell me what indicator you use that is long enough to reach in to the throat and an additional 2".
