PDX delivered 3 different sets of human portraits, two of which require no DLC. If you used one new human portrait and one legacy portrait, it would make it more clear that the game treats them as different species.
I am pretty sure the exact point is that two identical species using the same portrait will be treated by the game as different species just due to them being in two different starting empires. Which I am pretty sure is not WAD but an oversight (as the game was supposed to treat them as the same, but an update might have broken something).