Is This Common For a Custom-Built Torque Converter???

It is strange for a custom built converter not to have the correct bolt pattern.
Custom converters are built to the information given the builder by the customer. Given the wrong information, the converter will be wrong. I once had a customer screaming at me that his converter wasn't fitting properly. I got the spec. sheet he had filled in and looked it over. I went over what he'd put down on the sheet with him. When I got to the question, do you have a mid-plate and what thickness is it, it was blank. He forgot to note on his spec. sheet, he had a 3/16" midplate. Errors can happen from either party.
It's good to see that you are getting a refund.