That is not how I read the law, but I am not an attorney. Its reasonable to assume that the tune caused the issue, however the simple act of re-flashing the ECU should not automatically end the warranty. The key word in my mind is "warrantor can show". So can they show the tune caused the issue. LIke I said, maybe they can, the article makes no mention simply that the ECU was flashed.
Of course all that really matters is what you can convince a court, if you have the money to get there. I have always viewed factory warranties as not worth the paper there written on anyway. The OEM or dealer will deny what they want to deny.
"The federal minimum standards for full warranties are waived if the warrantor can show that the problem associated with a warranted consumer product was caused by damage while in the possession of the consumer, or by unreasonable use, including a failure to provide reasonable and necessary maintenance." https://en.wikipedia.org/wiki/Magnuson–Moss_Warranty_Act