The reason why these units acquire population cost is because there are already 2 cards with natives that can be used indefinitely (14 habsburg allies + Army of the Circle). I had already discussed this before in these forums:
The new Letter from Germany and France that allows you with a royal house (NATIVE EUROPEAN POST) should work as it is with the Incas or Ethiopia, to be viable
Germany new cards - #6 by OperaticShip743
Moving it to age 1 was nice, plus it grants a native embassy.
This is designed so that it is not unbalanced in the late game (I guess), so my proposal would be that the population cost is not necessary until the imperial age.