Can they make these claims in court? Sure they can. Their job is to obtain a conviction.
Can you defend against these claims? I would hope so. If you have modified all your guns for the sole purpose of killing someone, then you might have a problem. If you made these modifications for other reasons (i.e., sporterize the gun, make it smoother to shoot, more capacity for target shooting) and you have a good defense attorney, I would think the points of the prosecutor are moot.
I agree with PBP on his comment (Although I am going to ask a friend who is in the defense business if he has heard of such a case) and think it is just a coffee table lawyer spouting off.
Also, please consider, the type of guy who breaks into your house and threatens you, or your family, probably is not the stellar citizen who is going to hire an attorney to sue you because you shot him with an 18" barrelled shotgun as opposed to the 24' barrels one.
Inside Every Bright Idea Is The 50% Probability Of A Disaster Waiting To Happen.