This note: "to avoid duplicate commissions between agents and affiliates"...

Then money is being cut from independent affiliates to in-house agents? Did their wages get slashed by 50% to compensate for sales recession, and this is a way to compensate? =D

$100 is a very common payout limit. Anything above it will make sure nobody will become a random affiliate, and you loose all the little referrals in the process.