We know of at least one significant part of the problem is that the population is incorrectly calculated when a AI species migrates, resulting in the part of the population that stays in the patch receiving all of the penalty calculated for the population. I have observed it completely eliminating the population in a patch due to this.
Decreasing the Darwinian penalty would also help from what I have seen with a brief test, though a better fix would be to make the penalty scale with the size of the population so that larger organisms are not unfairly penalized by having naturally smaller max population sizes. I think this might be the main problem that causes the populations to crash.
I was discussing this with GameDungeon on the discord a while back (Discord link) but I have not had the opportunity to look into it any further, and I don’t think I can get to it this release cycle.