First of all dealers are wised up to the ECU mapping now so if you have APR, it's just the matter of playing with the stalks to find out what you've got in there.
Suspension mods are common, dealer only reject your warranty only to the related mods, Example: Lower suspension messed up the xenon leveler, so if something broke along that line they won't fix it under warranty.
I would check around for a mod friendly dealer first before you throw yourself into the job. Go on your regional forum and ask you fellow vdubber which dealer worth going into.
A note about mod-friendly dealer though, Every dealer have their own business philosophy, some open their doors to heavy mod cars don't mean they will throw everything into the warranty as a favor. It's just another way of getting business/new business.