From what I've read a vehicle has to be in the "historic" category to qualify for zero vehicle excise duty.
Vehicles which are 'substantially changed' don't qualify as historic under the new rules unless the modifications were carried out over 30 years ago. As far as I can tell the two are linked.
However it will be up to vehicle owners to decided if their vehicles are substantially changed or not. How you would go about proving or disproving when modifications were carried out is anyone's guess.