Even when filing by mail, you don't attach a 1099-R unless it has withholding.
Your problem is that the custodian of the retirement funds didn't send the proper documentation to the IRS, that's where you should be complaining.
E-filing is designed not to include any documents. There are very limited tax situations where the IRS wants you to mail a paper copy of a form after e-filing, and those do not include mis-matched 1099 information. Turbotax has also made an intentional decision not to allow any PDF attachments, for various reasons that may or may not make sense to you, but it is their decision. And, if you used different software and started randomly attaching documents to your e-filed return just in case they were needed, there is a good chance the IRS would ignore them or lose them. Just from experience.
