Have you tried for a workaround, as implied in that report?
When you change the Primary setting, do another fake (or not) modification to that monitor and Apply. I am not sure this would work (not clear to me in the comments… ).
I took the weekend for doing more test and looks like is working now (without any change)
Probably there is something in my little code that prevent it to work in some case. I will have a look when I have time.
Anyway thanks for pointing me in the right direction.
I hope the bug is fixed soon in gnome so I won’t need those kind of workaround.