Actually not really… Unless I misunderstood the point mentioned in your comment.
We had a Peatio based exchange, and we never had that issue. I mean there was no need to deduct the withdrawal fee from the deposits. This is a fact.
We used both a stand-alone wallet and a third party service: Bitgo . The stand-alone was for the erc20 tokens that are not supported by Bitgo.
There is a fee deducted from the wallet for creating a new erc20 address to users. This is solved by having ETH balance in the stand-alone wallet.
Regards…