AI computes
"Plot Found Values" and considers a lot of acpects.
(Ocean Access, Food, other Yields, Bonus Ressources in full City Radius, Rivers, ...)
Settling near Natives is generally not something that AI is afraid of - it has minimal impact on its decision.
(The Plot however is removed from "Plot Found Value" calculation, because AI can not get Yields from it.)
AI of course also has to consider the
"min distance" between European cities.
If we mess with it and
try to force AI to settle away from Natives, it might lead to
AIs not founding enough settlements.
The result will thus most likely be a lot worse that the current situation.
Summary:
Food, Yields, Bonus Ressources, Rivers, Ocean Access, ... are the most important factors.
Vicinity to Natives is definitely not - it is just a "minor factor" that the AI logic only considers as a side effect (of on plot less for "plot found value").
There is AI logic to calculate good spots to settle and it is actually
pretty good for an AI logic.
Of course however it does
not "think like a Human" and to expect something like that is unreaslistic.
I see absolutely no problem there.

It has been working perfectly fine so far.
By the way:
Nothing in the logic of "Europeans founding City" considering "Plot Values" has been changed to my knowledge.
(At least I did not and
@devolution would most likely have told so if he would have.)