@CalClassKen 

"It's easy enough to credit the customer $100, but if I want to send them a check for that amount it is impossible to show that payment (a banking tx) in the customer view so there's no way to see the events that took place when viewing the customer data."

If you're issuing a refund payment, create a Refund Receipt (New > Refund Receipt) with a note in the memo field.  That will show under the customer's account and you can easily see why it was issued.