I will look into it more closely, but at first sight one thing which bugs me is the way you overrate Blissey in both analyses. In GSC, Blissey kind of sucks. All that SpD is kinda useless without Natural Cure protecting you from Toxic. Moreover, she's a constant invite for Snorlax and friends to come in and wreak havoc, and unlike Raikou and Snorlax (the most popular answers to special sweepers in GSC), she lacks phazing moves or a true threatening presence. Skarmbliss stormed the metagame only from RSE on, it is not a concept which has real place in GSC.
Talked to Earthworm, he's pretty sure damage calcs are the same as ADV and DPP, with the exception of critical hits. Just keep in mind when using the damage calculator on the front page that all of the stats across the board of the Pokemon are at 248 EVs with a neutral nature. So the defending Pokemon would have 248 HP EVs and 248 EVs of whatever defense EVs you're using, as well as for attacking.