When using custom Board settings in XPE, calculated junction temperature is much lower than board temperature and Theta JA drops (0.1 - 0.6 C/W for this case when board temperature varied between 85 -125 deg C).
Ambient temperature = 85 deg C
Airflow = 0 LFM
Theta JB = 2.0 deg C/W
Board temperature = 125 deg C.
As a workaround, add a custom heat sink to the spreadsheet to fix the issue. For this specific package, that is Theta JA = 6.1 C/W in still air.
In general, using a custom Theta SA with airflow should calculate package Theta JA close to the same, as there is no heat sink in the above setup.