Don't worry about it.
Get familiar with this:
Magnusson-Moss Warranty Act
Basically, the burden of proof is on the dealer to prove that the modifications/parts installed are directly responsible for the failure.
I.E. A suspension system cannot be blamed for the air conditioning, but a case can be made that oversize tires contributed to a transmission failure.
Each dealership's Service Manager can interpret the data as they wish, which is why Toyota provides a system for arbitrating complaints.
My advice is to discuss your concerns with your service manager prior to installing the suspension.
He may want to install at the dealership- this is certainly not required, but if that's what it takes to avoid a conflict he may tie your hands. If he seems difficult to begin with, interview several service managers until you find one that is cool.
It helps if you are a regular customer
