"attaching the PDF to E-File is the only option"

Another option is an envelope addressed to IRS, with a stamp on it.  

The 504 notice isn't the trigger in most cases for requesting a Collection Due Process hearing.  That's the Form 12153.  If you file one now, IRS will probably tell you it's premature, but it will probably freeze the account.  File it again if you get the notice that says your 30-day deadline has started.  

This is the second post today that describes an amended return filed when the original was not prepared by the same practitioner.  Maybe IRS is considering it a second return and adding the income amounts together?  I don't really understand the aversion to paper filing of amended returns, which would make such confusion less likely, especially when no refund is involved.