For them not to cover it, they have to prove it came from doing the exhaust.
Get the foreign objects looked at by someone independent. See what their opinion is.
Actually Holden is not obligated to "prove" their view. It's their warranty and their product and the warranty is subject to conditions. They only need to argue that the foreign material entered the engine as a result of the unauthorised work carried out and the unauthorised parts fitted to the car. The obligation is on you, the claimant, to demonstrate otherwise if you want to challenge their opinion. If you wish to contest the warranty rejection (in Court) you will need many 000's of dollars and some pretty good evidence.
Your comment about the possibility of foreign material possibly entering the engine after removal of spark plugs during exhaust fitting sounds like just one plausible explanation and the metal need not even match anything on the car. If the metal fragments found matches any metal on the aftermarket exhaust it's pretty definitive as is the owner's advice that the problem arose within weeks of the exhaust mods being carried out.
The owner has not mentioned if anything else on the car might have been fiddled with which might be a factor. The metal fragments - described as 1/4 of a 5 cent piece - are thin and small and possibly quite light.
If people value their warranty, and they should, this is another very good example on this Forum of the costly financial risk you are taking if you modify your car when it is under warranty. You just never know what might crop up on your car over 3 years and if you modify it during the warranty period you are potentially leaving yourself very exposed whether you like this or not. Bitching about Holden's stance won't help one bit and you are starting from a position of disadvantage.
If I manufactured and sold a product with a warranty, I would not be happy for buyers to take my product, modify it under warranty , and then come back and ask me to fix it at my cost when a problem cropped up which had a possible connection with the unauthorised modification.