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An ioun torches caster level doesn't matter one bit. What matters is the relative spell levels; a continual flame spell has a spell level of 2 if created by a sorc/wiz/arcanist, 3 if created by anyone else. If it's a random item found or bought then you assume the lower i.e. 2.
Darkness is a 2nd level spell so normally this will cancel out the continual flame and the light level without spells in the area will apply.
Deeper darkness is a 3rd level spell, and against a normal ioun torch it wins and the full effect of deeper darkness applies.