I don't have a master system, but I have two light phasers, a Mega SD and a Mega Everdrive X5 running through a pair of model 1 Genesis consoles. One of the consoles is running through hd retrovision component cables into a 32 inch Sony Trinitron and the other console is running through composite into a 27 inch Toshiba CRT.
Weirdly, the guns are iron sight accurate through the composite line into the Toshiba and consistently shooting just to the right of the iron sights through the component lines into the Trinitron. This is consistent across all games and both guns. I haven't done extensive testing to try different cables and switching consoles around, but it's very strange behavior.
Anyway, on the Toshiba, the guns are pixel perfect accurate with no calibration, but unfortunately the phaser light gun games tend to bore me with their repetition and lack of personality.