If you fail the check that means you are a prohibited person, so it doesn't matter if the rifle you have has been made into an SBR yet or not, you are a felon (or other prohibited person) in possession of a firearm. How do they handle that now?
Yes it does matter. The former was sold to you after completing a 4473, to the best of your knowledge you are legal to possess a firearm.
If you get declined on an NFA application, when you're already in possession of an NFA firearm, you're unlawfully in possession of an NFA item and the ATF now has evidence to pursue you. And if they do pursue you, you will lose your firearms rights entirely.
How do they handle that? Ask the people at Waco... Oh wait, they're dead.