In terms of creating the observed weird population growth behavior, the thing that intensifies the problem is that you don't even NEED an empire with Xeno-Compatibilty to cause that issue. One of the events that can trigger with the Caravaneers is the creation of a cross-bred species.
Therefore, even if no one ever takes up Xeno-compatibility at all, if this event fires a few times (each in a different empire), it could create several new cross-breed species. And then if you have migration treaties with those empires, you have BOTH their main species AND the cross-breed species that can migrate to your empire and cause the aforementioned issues of shutting down the growth of other species with larger populations almost entirely until they reach comparable numbers.
Ouch. Hadn't realised that - I'd just assumed those damned space-elves[1] were gettin' thei freak on, but that probably made it even worse, then.
[1]Who I'd specifically force-spawned so there'd be one xenophiliac for my megacorp - naturally they spawed across the literal other side of the galazy and left me surrouned by maruaders, FEs, MEs, xenophobes and xenophobe mege-corps...