The holding fee is nothing to do with you at all, and you are not entitled to any of it. However, it should have been deducted either from the first month's rent or the deposit - it would have no impact on the money you get. If the tenant had not taken the flat, the agent would have been entitled to keep this fee (provided he followed the strictures of the law).
If the tenant has not had his holding fee returned then he should pursue it.
The letting agent has two contracts with two sets of terms and conditions - one with you and another with the tenant. Late rental charges are common, and you are not entitled to 90% of that.
In all fairness, 10% is very cheap so he has to make his money from the tenant too.
Read the contract you have with the letting agent. All the terms and conditions will be there.