i've gone for service with all the mods in my sig. So far so good. No issues to date. They still honor the maintenance schedule and any warranty issues. Mind u, i dont have a tune. But i have quite a number of other mods on my car.
Current: 2013 F10 M5 & 2013 GLK350
997.1 GT3RS (gone)
2009 WRX STI (gone)
e92 M3 (gone)