I don't know how the low pop bonus is calculated or what conditions need to occur for it to be given to a faction, but it would seem that it is being applied even when a faction is pop-locked:
These screenshots are from the current campaign. They were taken within seconds of each other, and after the score evaluation, but the conditions were the same before the eval and the points appear to have been awarded (which is what prompted me to take the screenshots). I and others I've played with have been noticing this for the last several weeks, though I've no idea how long this has been going on. This needs to be fixed, or the low pop bonus should be scrapped.