Common sense IMO.
My guess is that they will use the argument that if you are using lowered (tougher?) suspension, you are more likely to add wear to other parts of the car over using normal suspension, and will therefore refuse to carry out any work, as it may have been caused by the harder ride.
Whether or not that is the case is a different matter.
It's already a nightmare trying to get anyone to do anything under warrenty, why would you want to make that harder?
If you're not bothered about the warrenty then do it, if you need the warrenty, or want to keep the warrenty, don't do it.