I installed Tokico D-specs on my 2011 Mustang
and started experiencing clunking in the front end, but Ford still replaced both Front Control Arms without a problem. They said the installation of the Tokico's could not have caused the control arm issue, so replacing wasn't an issue.
As usual, most dealers should try to explain why any said aftermarket part caused the related warranty claim to be denied. You don't simply "void" a entire suspension warranty due to shocks and springs. If I had a problem, I would probably re-install the OE parts and then have an them make an untainted, unbiased, review of the problem for warranty review. It is too easy for them to "blame" the problem on the aftermarket part.