While not neccessarily a complete list, the main benefits of using deposit are below. 

(1) As explained here, there are monthly auction spend limits for direct payment on JDirectItems Auction. You can get around this, by using your deposit to bid on items. 

(2) If an item you have paid for is cancelled and is due a refund, if paying by deposit, that refund will go back to your deposit (as long as it has not been released). You can then use those funds for another purchase, rather than it being refunded all the way back to your credit card/paypal account. This has the benefit of:

• The funds will be available instantly for another purchase.
• You may be able to avoid multiple payment/refund transactions with your credit card and so potentially save transaction fees that your payment providor may charge you.

With the above in mind, the deposit is particularly suited for the below types of customers::

• JDirectItems Auction users: If losing an auction, the funds will go back to your deposit, ready for bidding on another item straight away!
• Users who wish to negotiate price with Mercari/Rakuma sellers: As shown here, to negotiate price, charge 1 payment first has to be made. By using deposit for payment, should agreement not be reached, your refunded charge 1 will be available in your deposit for use again straight away.