I would say it depends on the dealer and what specific problems arise in the future.
Logiclly, I now have no expectation that my struts are covered... and I would bet that if I managed to mushroom a strut tower, it might be debatable.
It was a change I knew I was going to do out of the box. The car was either going to get the MINI sport suspension and lowered with springs ($500 + $480 for installed springs), or come with statndard suspension and get a full coilover setup and stiffer rear swaybar ($2000+). Either way would have the same potential warranty considerations. I took what I believe to be the less expensive option.
I really like the results so far (both loooks and handling) and wouldn't consider owning the new R56 without one of these options.