We are using custom coins only so why should be activate account using XML?
The network need to lock base reserve and charge minimum transaction fees to prevent transactions spamming by bad actors. It's essential because all transactions end up in history archives and operational databases, resulting in significant blockchain size increase. Validators have to pay more for storage and move costly servers in order to handle ever increasing blockchain.
Is there any way to manage all customers account using a single private key?
You can track all your customers internally, in your database. It requires additional coding and database maintenance, however this approach allows you to use single Stellar account for all deposits and withdrawals.