Why is AutoPIPE automatically using ASME B31.J for SIF and flexibility calculations in ASME B31.1 2020?
Because that is what the piping code requires. See ASME B31.1 2020. Stress calculation for sustained, occasional, and thermal loads in B31.1 (2020) requires the use of flexibility and stress intensification factors from B31.J
ASME B31.1 Piping Code Calculation Issues
Bentley AutoPIPE