I don't know if anyone has actually measured any official loss, based upon controlled testing where identical conditions are repeated between stock and stage 1.
In reality, stage 1 tuning requires (in your case) a re-jet of the carburator to richen up the mixture. Opening up the exhaust and the air cleaner allows more air, hence the need for more fuel or you'll burn up the engine from running too lean.
The other thing that can affect your gas mileage is the pure fun of additional horsepower and the inabbility to not run your bike like you stole it! There goes gas mileage!
My 2006 XL1200C has the stage 1 upgrades (SE II pipes and SE air cleaner) and I still get 50-52 on the highway, and around 45-48 in town running around. Provided I keep out of the throttle!