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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.
As AVR says, against a typical Ioun Torch will lose out to a deeper darkness (2nd vs 3rd level spell). Which is why you probably want to pay the extra GP when it's crafted (assuming you bought it and didn't find it) and have it Heightened.
Yeah, the real answer is you buy a dull grey ioun stone and pay someone to cast Heightened (4th level) continual flame on it. The total cost is 305 gp.
Now, the only way deeper darkness works is if they've heightened it, which is probably unlikely.