It's not lower as much as it's scooped. Because of the mid-range cut, it doesn't push the amp front end as much as 1/3/5. Also, the human ear is most sensitive to mid-range sounds, so to our ear it sounds quieter. I haven't measured it, but I suspect signal-wise it's comparable.
Practically speaking I usually wind up turning the volume up a touch in 2/4 if I'm trying to maintain a consistent crunch tone, otherwise the mid cut tends to clean the tone up a little.
Edit: The foregoing holds true as well for my Sabre, which is wired similarly, and for that matter, my Strat in positions 2/4. It's a common phenomenon.