Looking for confirmation as to how the trunk weatherstripping is installed on a 69 GTX or other B-body. I believe the groove goes to the outside(and down at the rear of the car). Correct?

Yes correct groove goes on the outside for water drainage and it comes together at the trunk lock area.

Thanks. I also seem to remember that the butt joint on the weatherstripping is typically offset a couple inches from the latch and the center of the lip. True?

correct on both counts!