Customers deposit multiple cheques at the same time, not always from one customer. To keep the paper trail consistent with bank reconciliation customers would like this feature enabled. You are currently restricted on one customer and their receivables only.
There is an easy way to accomplish this. Create a "Deposit Account" as a bank account in your chart of accounts. Payments from customers can be deposited to that deposit account and then when you do the mass deposit, you can just transfer that amount from your deposit account into your business bank account. That would provide an accurate audit trail and keep things organized and easier to reconcile.
You can make a deposit though with several RPs on it. It's not convenient for a large number of cheques, but I've done two or three different customers deposits in one deposit using various RPs.