They frequently are. Currently, same species mechanics are RIDICULOUSLY broken.

In my last CoM game, I took biological ascension, while the UNE went for mind over matter. Aside from the fact that the claims in the tooltip when they transcended (that all humans across the galaxy had unlocked psionic abilities) were false, when I conquered some worlds where humans had migrated, those UNE humans were treated as xenos and any attempt to make them not-xenos failed My other experiences haven't been much better.

The way the game keeps track of species simply doesn't work as it should. Rather than treat every species with the same portrait as the same species throughout the game, it creates new species for ascension paths and frequently seems to fail to recognize that two species with the same name and the same portrait should be part of the same species now that they are in the same empire.