I've been using the LUA RNG script to run this and this encounter is seriously unstable. What doesn't help is that manipulating a Moltres requires going through XD001 first and despite my calculations on trying to hit advances say "29992" after cutscene load, it doesn't always add up when the battle starts like it's deliberately trying to not give a flawless spread on the 2nd Pkmn slot.
I do know that its RNG IV+Nature spread is +7 after Rhydon and my past results were usually 3 or 1 out.
XD Lugia with LUA Script isn't too bad and I've managed to get Shiny Beasts in Colosseum.
Update:
I tried a different stat spread with an odd number advances frame and managed to get it, I've noticed that from cutscene to Rhydon + Moltres spawn, it's not always 10+ to Rhydon and then +7 to Moltres (17 advances). It could be +11 Rhydon to +7 Moltres (18 advances)
My advances counter during a cutscene was under my estimate and still managed to get it due to advancing more than usual when the battle started.
Good luck to anyone pulling this off on retail console.