Can setup fees be waived or ignored for certain customers?

The setup fee cannot be edited or enabled/disabled for the individual customer. This is a field that is configured at the plan level and will always apply immediately upon the subscription being purchased. A way to bypass this and wave the fee would be through the user of either a flat-rate coupon for the amount of the setup fee or by adding a credit to the customer's account for the same amount. This will still show the setup fee included in the invoice that's generated and billed to the customer, but the coupon or credit you decide to give will be able to ensure that the customer is not billed for the setup fee amount.