You are not supposed to do anything to them. If the author asks, do it
I mean, seriously, most mods feature author's graphics and tweaks, and it doesn't show where they belong to. I've played Dark Dwarves and it's the same Dwarf Fortress with different contents, I mean I feel like I live in the same world, just with more things and features.
As Blakmane said, it's on par with my DFCP (lol Blakmane, I have 30-40 Kb more
) in terms of gameplay.
Also add DiG DeepeR to the list.
P.S. Even Kobolds Camp feels more like a total conversion... Unless the mod introduces a totally new world/universe it's not a total conversion (and the fact how much it adds means nothing... well, besides the fact that it's a good mod