The max height data in the Tamriel worldspace has had every DLC tweak the information in some way, which has led to the information being out of sync since at least 2013. Probably longer.
After it was analyzed by Elemental (a user on the xEdit Discord) it was determined that the USSEP should have some adjustments made to the MHDT subrecord for Tamriel. In addition to this 4 individual cells needed to be edited to make the data generate correctly. Cell 28,-21 at Treva's Watch, two cells at Robber's Gorge, and one more somewhere near the southwest corner of the map.
This data affects how dragons fly around and avoid obstacles so it should make everything work smoothly now.