I'd do it even if deepening the slots will work. The bone nut's better, so why not ;-)
It would not even have occurred to me to return the defective kit unless asked to do so. Your idea seems like a very measured response.At first I thought after they get back to me with reasonable solution ( Atleast a 16 Aud refund for the missing file) to the problem, I shall ship one of those guitar Body and neck back to them.