Just to pile on here: I'm having the same problem.
I have an early 2009 Mac Pro, single-socket. I have upgraded to a single hexcore Xeon and 5,1 firmware. I have the original GT120 in the first slot, a Quadro FX570 in the other x16 slot, and an identical FX570 in one of the slower slots. I normally drive four monitors, three 2560x1440 panels and one 1920x1200 panel (the latter from the quadro in the x4 slot).
Right after upgrading to 10.11 I get the crashes back to the login screen seconds after the desktop loads. I can't really do anything. I've confirmed that dropping to a single card (with one or two monitors) makes it work again.
I haven't tried either of the two proposed solutions because I can't possibly work with the danger of being logged out in the middle of something. I'm heavily dependent on all four displays, but stability is important. So, I'm going to wait for apple to do something, or roll back to 10.10 if I have to.
I filed a bug and included my system report. As a software developer, I definitely encourage everyone to make sure they've opened a bug for this!