Payment Terms for Customer Agreement

You can define different terms on the invoice itself whenever it is created, but that would have to be done manually.  I don’t know of a way to tie individual and varying terms to the customer agreement that would only pull through on the invoices associated with that agreement.  The payment terms established on the customer account are always going to be the default pulled through on each invoice irrespective of whether it is originating from a customer order line, customer agreement connected order line, or a manually entered invoice.

Yes, that could possibly work.  A custom attribute on the agreement that is then read for a new invoice created for that customer and sits close to the normal payment terms field on the invoice.  The person doing the invoicing would then have verify every invoice to notice the terms were different and change the payment terms at that time.  There might be further validation on the invoice that could be done before printing or something, but that depends a bit on the work flow for that process.