Fixed both problems.
Jitter: replaced the 1.8V Vccaux switcher with a linear regulator.
Temperature-dependant crashing: I found an oscillation on the Zynq 1v core power supply, about 100 mV p-p and 80 KHz. Putting a lot more capacitance at the switcher output kills that and makes the crash go away. The regulator design followed a chart in the LTM8078 data sheet. A Spice sim with the original values looks stable, no oscillation and a clean load-step recovery.
There are other indications that ADI's Spice model of the LTM8078 is less than perfect. I think ADI is struggling to add a lot of new parts to the LT Spice libraries. Mike E in an interview suggested that rushing them out was compromising quality. Then he quit.
Glad I fixed this this way. Guys were snooping the AXIbus and Linux at great expense and no progress.