Getting the probabilities could be very difficult though, especially for issues that never occurred before.
For issues that have never occurred before, probabilities are the wrong tool. The right thing to do is list all the behaviour the vehicle must never exhibit and think of ways it still might, despite all redundancies -- maybe even despite every single component working as intended.
Lots of mission failures in history were caused by unexpected interactions between fully functional components. Probabilities of failures don't help with that.
That is what you hire an army of engineers for.
The fault tolerance is mostly focused on background radiation flipping bits. We've got half a century of data on the frequency of those upsets and the extent to which they're correlated under different space conditions for that, not to mention the ability to irradiate prototypes of the flight computer with representative amounts of shielding in ground based facilities...