This is a bit of a tricky one.
The 3-C is more their level of influence outside the Warp while being actively inhibited by the Emperor, as even so, they can still actively manipulate large portions of the galaxy to their will.
The Low 2-C is based on what would happen if the Emperor was not there to hold them back. Basically, we're told that the influence of Chaos would burst forth into the universe, collapsing the Materium's dimensional walls and annihilating it utterly, making it just another part of the Warp.
Now it is true that this is because of the Warp breaching realspace, but it is Chaos' influence doing so, and is exactly what would happen were there not an equally powerful being constantly holding them back with his colossal psychic presence. Because of this, their influence would only be limited to 3-C were we to assume the universe they were trying to influence contained the God Emperor. In any other universe, they could presumably just destroy it were there not something in their way.
Here's where the problem lies, though. They would be destroying a universe currently outside of their jurisdiction, but would technically be doing so with the Warp (which is themselves). On top of this, we don't know their exact level of influence on the countless other universes connected to the Warp. Since the Daemons codex mentions that the Emperor was the strongest entity in existence at the height of his psychic power (as in, greater than any single Chaos God, which is why they were genuinely concerned about him), I strongly doubt even a notable fraction of said other universes have Emperor-level beings restricting the Chaos Gods' influence.
Because of this, perhaps the best rating for the Gods' influence outside the Warp would be something along the lines of "3-C while restricted, Unknown while unrestricted".