When customer accounts are activated, they're automatically charged for the security deposit fee or setup fee associated with their chosen plans. You do have the option to prevent this from happening by either:
1. (Easiest method) You can manually activate the customer from your end, apply an initial credit amount to cover the security deposit amount, and keep the 'apply setup fee' box unticked. Screenshot below:
2. If the customer will activate their account from their end. You will need to create a one time use coupon code specifically for this customer to apply while they're resubscribing their account. The coupon code amount should cover the security deposit and the setup fee amounts.