Ok, I've tried loading that first autosave and playing around from there; I did manage to get one desync but when I reloaded and did the same thing again it didn't reproduce. To actually nail it I need it to happen every time (or at least often enough that it doesn't take me days to retest). In my last test it ran all the way from when I loaded, through a full two-stage assault of that first core world, to just past the deploying of the CPA with no problems before I just stopped it to look for a more fruitful angle.
I'll try some of the more specific things you mentioned above, but thus far none are actually reproducing desyncs (the one I got came the same instant I destroyed a mass driver, for some reason, though the same thing the next time didn't).