As a fractional accounting team that supports businesses on NetSuite, this journal entry as a payment idea seems scary. If you start recording multiple customer payments via JE, I would think that would really mess up the bank reconciliation then.
If your team is looking to automate this, I can't understand why importing hundreds of customer payments is a bad thing? If the concern is they then need to select a bunch of payments to record a bank deposit, then a script could be used for that piece.