Yes, CIWS break all the rules. They will intercept inside atmosphere, they will intercept missiles that launch - fly - hit inside a 5 sec phase and what was the third special thing about them...
Well, I can't remember. Someone will add it here, I'm sure.
IIRC, CIWS always work because they're programmed to be "special" in a number of ways, and so not subject to the normal restrictions. I believe the in-game reasoning for this is that they work at such a short range that the atmosphere wouldn't affect their operations.
I feel like I have seen this answered somewhere but I could not find it on the forums or the wiki.
When using PDCs, do CIWS work on PDCs that are on a planet with an atmosphere? I have seen CIWS work on a PDC deployed on a body without atmosphere, but when a planet has an atmosphere, do CIWS always work, or are they reduced by the atmosphere the same way that other directed energy weapons are reduced?