The reality is most dealers will use any excuse they can find/see to deny a waranty claim.
You can have all the magnussen/moss acts ect but in the end its going to be you ie someone generally not trained/qualified or experienced in the industry arguing your point against experienced trained qualified persons.
Flash tuning is probably one of the safest mods as you can flash back to stock easily and their is no evidence to prove it was flashed or what was flashed. (please provide me with location of flash counter
,) their is a timer for last DTC/CEL reset and distance since DTC/CEL reset.
The turbo/supercharger under the bonnet might give it away though
If you lower your car and put on 10" wheels it would be pretty easy for them to prove the axles broke due increased traction and the suspension geometry change.
Any mod you do risks warranty denial on the modded part and associated parts/systems.