A bunch of the options cause lag spikes when changed (e.g. Ambient Light, Radiosity, mat_specular). They're more severe on larger maps, so if it's just larger maps it might be because too much is being loaded in/changed at once. If it's every map (including ones like gm_construct) then I'm not really sure what would cause this. Either way I don't think I can really do anything to help other than suggesting you try using smaller maps, fewer changed values, or fewer entities.

Everything that causes any lag in this addon is a result of changing an existing console command or calling an existing function, which I don't have any way to optimize.

(Also the fog editor shouldn't have any effect on the light/environment editor, there isn't any overlap in what they do/what functions they use. If it did I'd be very surprised)

I agree that it might just be due to too much being loaded in at once. Could it be possible that a slight delay is added? Maybe a way to wait for the game to load and then apply the lighting changes?