If you check this option, the invoice basis will automatically be put in pending status (status 3) when the delivery is made to the current customer. You cannot print such an invoice before you have changed the invoice basis status to 1.
There is a general setting that determines if the Invoice is Pending option should be set by default when registering new customers. This setting is called Status 'Pending' on invoice basis for new customers and can be found under Orders / Quotes under the Sales tab in the Settings procedure.
You can make exceptions for individual orders in the Register Customer Order procedure. However, the setting in the Update Customer procedure is selected by default.