[WhiteyChev]

It's mostly common sense. Warranty is designed to cover defects in workmanship & quality.
Engineers spend a ton of time making sure all components work properly together, from A to Z. Safety, performance, comfort, longevity, fuel efficiency etc are just some of the considerations.

When a change is made, it has potential to affect things downstream. That would not be a defect, but a material change to the highly qualified 'status quo'.
A transmission designed to handle 250 HP could very well fail at 350 HP. A manufacturer could design for 350HP, but then we'd be whining about the cost of it! Or they simply wouldn't sell due to non competitiveness, wouldn't continue to produce & we'd have nothing to modify!
A front air deflector on the hood can affect MPG & more likely, cabin wind noise.
Like life - everything is a trade off.

IMO any issue at your dealer is usually a misunderstanding/ miscommunication of some sort, warranty work is mostly the best work. The price is set fairly & the manufacturer pays on time & without complaint or negotiation. Not always the case with customer pay.
They cannot/ should not lie to the manaufacturer about diagnosis/ cause - ever. This would jeopardize their future unnecessarily. But when/ if justifiable, should gladly look after their customers. That's kinda how it works.

If you make changes, there are risks. Know that & enjoy your car! However that may affect you. There's no free lunch & life is short.