How will First Contact mechanics behave with two species with same name + portrait?

[Alfray Stryke]

Will it act as if the other is a "Lost Colony"? Will they be recognised as the same species during a first contact event?

EDIT: The reason I ask this is because I like to make custom versions of the UNE and Commonwealth of Man, but I still want them to recognise each other as human.

Empires that have the same primary species should have an easier time contacting each other regardless of custom flags set - this even includes if one of the empires in question is a fanatic purifier.

And yes, editing and saving the UNE and COM keeps their custom flags (and thus an edited COM even gets the Hunt for the Hyacinth mission).