When you modify the suspension a lot you drastically change the way it will handle and how long it will last. Many modifications are outright dangerous.
Most lowering jobs I have seen would probably be considered unsafe by the factory and by police and state inspections. Lowering can safely be done with quality parts and good engineering thinking, but most guys seem to chop parts, torch springs and use parts that aren't right for that car.
You can't blame the manufacturer if you replaced(or worse removed) factory parts with parts that are not to spec and in their opinion a product liability lawsuit waiting to happen. Also they are concerned that you will blame factory parts for wearing out when in reality you changed the geometry of the suspension which can over stress components.
They cannot deny a claim say, for a faulty air conditioner or an engine that has failed coils just because you lowered it, but they have a right to deny any suspension issues and the tire company can deny coverage on the tires if your suspension geometry is wrong.
Even tire companies will only warranty tires that are within a specified range. Anyone using tires that are too big or too small may have to sign a wavier saying they know the tires may be unsafe and were changed against the advice of the tire mfg.
I have "been there done that" long ago and signed many waviers. But as I got older I realized that cars are safer and more reliable when you make minor improvements and changes, not major stuff like suspensions.
SEMA does have some certification programs where aftermarket parts are supposed to be legal and safe for a car and supposedly a dealer can only deny a claim that directly resulted from an aftermarket part. But still some dealers and state inspections will still disallow the changes. This is a kind of a grey zone still.
In my opinion minor stuff like simple engine and exhaust mods are OK, tire changes within reason OK. But lowering a car, especially if not done with proper engineering thought being put into it can be unsafe and cause a factory suspension to fail prematurely.
Just my opinion based upon hotrodding for many years in the 70s and lots of reading and tinkering since before I was legal to drive. Plus I do have an engineering background but not automotive, so it makes me nervous when I seen things that just ain't right.
Jim Henderson