Hey Leoreth, I checked Stability.py. The Religions stability penalty for Secularism is indeed mistaken. The lack of penalty is not assigned to Secularism, but to Scholasticism in some cases, and in other cases not assigned at all.
The most important line is the one about religions spread to cities affecting stability, where Mongolia is an exception. Every civ running Secularism should be added as exceptions, in addition to Mongolia.
I also think this stability "Normalization" thing should be removed. It is pointless, except it hides mistakes in the Stability calculations such as the religious stability mistakes I just reported.