They slapped Carl Long very hard and I think he had a Yates engine. He most likely never removed the heads or anything (probably forbidden by Yates). If they can do that to Long with his limitations, the penalties are fairly consistent. Note: The Long incident was not even a points paying event, and the engine was seized during practice.
I may have a different opinion on the harshness, but it doesnt matter, Nascar knows more about controlling rules than I do. Seems like Nascar is doing more to punish the CC and others now, but an unenforced rule is pointless.
I think Matt will rebound and make the chase, losing the 3 chase bonus points could be the biggest problem. But it is better for TRDs problem to be exposed now, they can address the problem, better calibrate their weights and quality controls now. That's better than discovery during the chase.
Thats all you can do, learn and move on, fair or unfair.