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i don't believe the RNG pauses. from my experience the RNG changes if you take any pokemon out of the daycare without putting a pair back in, possibly because the RNG changes by taking steps or encountering pokemon like last gen.
are IVs determined when eggs are created now? i've saved in front of the daycare several times and have noticed no change in IVs when picking up the same egg yet.
the yveltal i caught had perfect hp(201), attack(151), spatk(151), and speed(119) stats at level 50 according to the 126/131/95/131/98/99 base stats from pokemon showdown. so it's possible, may need to test this out more though.
can xerneas and yveltal be caught at a later time instead of at team flare's secret base? like how reshiram and zekrom could be caught later in dragonspiral tower in black & white if you had all your boxes maxed out with pokemon? i doubt anyone has tried this yet unless they got the game early...
i mentioned a dragon dance set because you asked in your additional comments/questions if not having a set-up sweeper would hurt your team. since you only have 1 pokemon with a physical fighting type move, chansey, and blissey somewhat, will wall your team well. salamence's outrage will only...
i think it would be a good idea to add dragon dance on salamence, like you mentioned. however this would possibly create problems against gliscor. switching hp ice over toxic on heatran may work, then giving ferrothorn toxic over thunder wave or leech seed if you need help against bulky walls...