Okay now that i spend more time with it (need to make a few maps for my game tomorrow) it is just saving the last cities features regardless of what is selected on the preview.
So I open up that map i just showed as an example, set it all to the features i want according to the preview, then save and close. I open a new settlement, and even though the preview of this second one shows no walls, no plaza, but a shanty town instead, it loads in walls and a plaza.
Does this help explain it a little better? Lol