Anyway, I'm not using Real Lights as I haven't been happy with the results when trying it/similar mods out previously, so I've missed that it adds lights to Varla and Welkynd stones until wrinklyninja mentioned it in another thread. I stripped everything except those changes from All Natural - Real Lights and it seems to work perfectly. Really cool IMO.
Should probably try Real Light BTW, it was years since I tried it the last time.
Dots and + signs are different things. You get a + for merged mods and a dot for mods that have stuff imported into the bashed patch - in both cases when the mods in question are unchecked in the mod list.