The text of the actual rule document referencing 922(r) was posted a few pages back. It's on page 246-247 and is pretty clear. I wouldn't say it's a theoretical interpretation. If the rule goes into effect, meaning pistols with braces installed retroactively become SBRs, then the 922(r) concern is real. The crime is assembling a rifle or shotgun in the banned configuration with more than 10 foreign parts. If installing the brace made the gun a rifle, then the crime was committed and can't be uncommitted unless the person made the pistol 922(r) compliant prior to installing the brace. Who would have done that and for what reason? Up until now, they told you installing a brace onto a pistol didn't make it into a rifle so 922(r) wasn't even a thought.
@HCM asked a good question upthread. While there is a statute in place preventing the government from prosecuting you criminally based on honest information you submitted while trying to comply with the NFA, we aren't familiar enough with the statute to know if it would prevent the government from civilly forfeiting the gun in question without reimbursement as contraband.