If you’re hunting for Arcanes:
lvl 12 explore mini-boss and mythic boss, give 1 guaranted (so you get 2 in 1 D12 run assuming you got enough mythstones for boss fight)
As for lower rairty stones:
It’s probably better to go with lower difficulty, because there isn’t anything explicitly written about lower rarity ones in 4.6 patch notes (apart that mini-boss battle has increased chance of dropping arcane stones and that this chance is applified by Explore difficulty setting)
More here:
my best hint would be: when hunting for runic traitstones, go with d1 or whatever difficulty that allows you to 1shot everything with AoE on first cast and just grind it quickly…