I have asked the same question about many of these type of videos. I'm sure they don't worry about the theory and just play what sounds good.
There's one I saw recently that tried to break down the time signatures of a Tool drum part, I'm pretty sure Danny Carey isn't sat there thinking about 4 different time signatures while he is playing! It's about feel and groove.
Edit - took this from Danny Carey's wiki entry
He has also stated that when he is playing to an odd time signature, he tries to drum to the "feel" of the song and establish general "inner pulse" for the given time signature instead of fully counting it out.