For example, if the user adds $100 to his ETH account and only withdraws $70, after a $20 commission, he is left with $10 on his account that he will never get to use.
You don't have to give the 70 dollars worth of ethereum from the address the user has deposited to. You can use the fund other users have deposited to process one's withdrawal.
Centralized exchanges usually move all the funds to their own wallet and use the fund in that wallet for processing withdrawals.
Also note that you should set a minimum for withdrawals and deposits.