I understand baseline heights and their adjustments with the top of plate with or without a birdsmouth cut. Even if you adjust the baseline height to make the top of plate value equate to the exact elevation that it is supposed to be, it does not work. But that is probably because the Auto Story Pole dimensions pull the room specifications rather than the roof.
Curious about the ceiling height change (36") versus maintaining the proper ceiling height (109.125"), I made a new plan with two equal structures. The one I made 36" ceilings with flat ceiling unchecked, and the other I made 109.125" ceilings with flat ceiling checked. I drew both roof planes manually. The 36" ceiling roof plane sat right at 157.75" correctly. The 109.125" roof plane obviously snapped to the 109.125" plate height and I adjusted it down by locking the pitch and adjusting the Baseline Height accordingly.
In the end, both ended up being on the money with the Auto Story Pole dimensions with 36" knee walls. It looks like something in my original file was throwing it off, but I am not sure what. I'll figure it out or redraw it.
Thanks for the help everyone.