Good job getting Freecad to run non linear solutions. I think with a .4mm flaw size, this ends up being a fracture mechanics research project. Just reading the Wiki page should show how much fun that would be.I can't understand why the manufacturer would try to defend using material yield to meet safety margins instead of the simple 3 mm fillet that solves the problem with straight forward linear analysis. At some point, maybe they should just stop digging the hole.Great work.
It may be interesting to run the 30MPa basic fill pressure case and see how much is above yield.I think your constraints are OK for what you are doing. This is an internal loads case. Constraining the model with a 6 degree of freedom connection to ground is sufficient. I think you have that on the right side of the o-ring block. As you have it, there is an artificial compression force on the o-ring block. That is not the high stress area. To be more representative you could add a cap disk to the threaded end, join it to your model as mentioned earlier and then ground your model there. That would add the axial load to the tube and remove the compression on the o-ring block. This may change the stress in the fillet.